From 2a534f3924c9a3ec59e53ba53c1ba57c7cc47a68 Mon Sep 17 00:00:00 2001 From: csbrasnett Date: Mon, 28 Oct 2024 11:26:40 +0100 Subject: [PATCH 1/6] add -name flag to allow for custom naming of input molecules --- bin/martinize2 | 10 +++++++++- vermouth/processors/name_moltype.py | 7 ++++--- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index 91eca3261..72f80215b 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -328,6 +328,14 @@ def entry(): "if instead all chains in the input file should be merged.\n" "Can be given multiple times for different groups of chains to merge.", ) + file_group.add_argument( + "-name", + dest="molname", + type=str, + default="molecule", + help="Name for the output molecule. If not specified, will default to 'molecule_{0..n}' for the number of" + " molecules in your system." + ) file_group.add_argument( "-resid", dest="resid_handling", @@ -1024,7 +1032,7 @@ def entry(): raise argparse.ArgumentError(chain_merging, message=("Multiple conflicting merging arguments given. " "Either specify -merge all or -merge A,B,C (+).")) - vermouth.NameMolType(deduplicate=not args.keep_duplicate_itp).run_system(system) + vermouth.NameMolType(deduplicate=not args.keep_duplicate_itp, molname=args.molname).run_system(system) defines = () # Apply a rubber band elastic network is required. diff --git a/vermouth/processors/name_moltype.py b/vermouth/processors/name_moltype.py index 0d6799fe6..fe6399301 100644 --- a/vermouth/processors/name_moltype.py +++ b/vermouth/processors/name_moltype.py @@ -58,9 +58,10 @@ class NameMolType(Processor): the molecule. """ # TODO: See issue #35 - def __init__(self, deduplicate=True, meta_key='moltype'): + def __init__(self, deduplicate=True, meta_key='moltype', molname='molecule'): self.deduplicate = deduplicate self.meta_key = meta_key + self.molname = molname super().__init__() def run_system(self, system): @@ -85,8 +86,8 @@ def _name_with_deduplication(self, system): group_id += 1 representatives.append((group_id, molecule)) match_id = group_id - molecule.meta[self.meta_key] = 'molecule_{}'.format(match_id) + molecule.meta[self.meta_key] = '{}_{}'.format(self.molname, match_id) def _name_without_deduplication(self, system): for molecule_id, molecule in enumerate(system.molecules): - molecule.meta[self.meta_key] = 'molecule_{}'.format(molecule_id) + molecule.meta[self.meta_key] = '{}_{}'.format(self.molname, molecule_id) From 2dd0a19dc3900b6fe01b7351d72b95d465016cf2 Mon Sep 17 00:00:00 2001 From: csbrasnett Date: Mon, 28 Oct 2024 11:57:01 +0100 Subject: [PATCH 2/6] remove -go-moltype argument. virtual go site atoms now inherit their names from the molecule name. Go pipeline merges all molecules anyway, so retaining individual molecule names shouldn't matter. --- bin/martinize2 | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index 72f80215b..4872dfb7d 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -564,12 +564,6 @@ def entry(): default=9.414, help=("The strength of the Go model structural bias in kJ/mol."), ) - go_group.add_argument( - "-go-moltype", - dest="govs_moltype", - default="molecule_0", - help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), - ) go_group.add_argument( "-go-low", dest="go_low", @@ -1000,11 +994,12 @@ def entry(): # Generate the Go model if required if args.go: + go_name_prefix = args.molname LOGGER.info("Reading Go model contact map.", type="step") go_map = read_go_map(args.go) LOGGER.info("Generating the Go model.", type="step") GoPipeline.run_system(system, - moltype=args.govs_moltype, + moltype=go_name_prefix, contact_map=go_map, cutoff_short=args.go_low, cutoff_long=args.go_up, From dd72bbaa1a028ed45aefbd7f661c69dc260a92e9 Mon Sep 17 00:00:00 2001 From: csbrasnett Date: Mon, 28 Oct 2024 13:01:14 +0100 Subject: [PATCH 3/6] update names in integration tests for go models --- .../lysozyme_GO/martinize2/go_atomtypes.itp | 258 ++++---- .../lysozyme_GO/martinize2/go_nbparams.itp | 518 +++++++-------- .../martinize2/go_atomtypes.itp | 258 ++++---- .../martinize2/go_nbparams.itp | 596 +++++++++--------- 4 files changed, 809 insertions(+), 821 deletions(-) diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp index bcbcf6145..3b028c477 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp @@ -1,130 +1,130 @@ [ atomtypes ] -molecule_0_1 0.0 0 A 0.00000000 0.00000000 -molecule_0_2 0.0 0 A 0.00000000 0.00000000 -molecule_0_3 0.0 0 A 0.00000000 0.00000000 -molecule_0_4 0.0 0 A 0.00000000 0.00000000 -molecule_0_5 0.0 0 A 0.00000000 0.00000000 -molecule_0_6 0.0 0 A 0.00000000 0.00000000 -molecule_0_7 0.0 0 A 0.00000000 0.00000000 -molecule_0_8 0.0 0 A 0.00000000 0.00000000 -molecule_0_9 0.0 0 A 0.00000000 0.00000000 -molecule_0_10 0.0 0 A 0.00000000 0.00000000 -molecule_0_11 0.0 0 A 0.00000000 0.00000000 -molecule_0_12 0.0 0 A 0.00000000 0.00000000 -molecule_0_13 0.0 0 A 0.00000000 0.00000000 -molecule_0_14 0.0 0 A 0.00000000 0.00000000 -molecule_0_15 0.0 0 A 0.00000000 0.00000000 -molecule_0_16 0.0 0 A 0.00000000 0.00000000 -molecule_0_17 0.0 0 A 0.00000000 0.00000000 -molecule_0_18 0.0 0 A 0.00000000 0.00000000 -molecule_0_19 0.0 0 A 0.00000000 0.00000000 -molecule_0_20 0.0 0 A 0.00000000 0.00000000 -molecule_0_21 0.0 0 A 0.00000000 0.00000000 -molecule_0_22 0.0 0 A 0.00000000 0.00000000 -molecule_0_23 0.0 0 A 0.00000000 0.00000000 -molecule_0_24 0.0 0 A 0.00000000 0.00000000 -molecule_0_25 0.0 0 A 0.00000000 0.00000000 -molecule_0_26 0.0 0 A 0.00000000 0.00000000 -molecule_0_27 0.0 0 A 0.00000000 0.00000000 -molecule_0_28 0.0 0 A 0.00000000 0.00000000 -molecule_0_29 0.0 0 A 0.00000000 0.00000000 -molecule_0_30 0.0 0 A 0.00000000 0.00000000 -molecule_0_31 0.0 0 A 0.00000000 0.00000000 -molecule_0_32 0.0 0 A 0.00000000 0.00000000 -molecule_0_33 0.0 0 A 0.00000000 0.00000000 -molecule_0_34 0.0 0 A 0.00000000 0.00000000 -molecule_0_35 0.0 0 A 0.00000000 0.00000000 -molecule_0_36 0.0 0 A 0.00000000 0.00000000 -molecule_0_37 0.0 0 A 0.00000000 0.00000000 -molecule_0_38 0.0 0 A 0.00000000 0.00000000 -molecule_0_39 0.0 0 A 0.00000000 0.00000000 -molecule_0_40 0.0 0 A 0.00000000 0.00000000 -molecule_0_41 0.0 0 A 0.00000000 0.00000000 -molecule_0_42 0.0 0 A 0.00000000 0.00000000 -molecule_0_43 0.0 0 A 0.00000000 0.00000000 -molecule_0_44 0.0 0 A 0.00000000 0.00000000 -molecule_0_45 0.0 0 A 0.00000000 0.00000000 -molecule_0_46 0.0 0 A 0.00000000 0.00000000 -molecule_0_47 0.0 0 A 0.00000000 0.00000000 -molecule_0_48 0.0 0 A 0.00000000 0.00000000 -molecule_0_49 0.0 0 A 0.00000000 0.00000000 -molecule_0_50 0.0 0 A 0.00000000 0.00000000 -molecule_0_51 0.0 0 A 0.00000000 0.00000000 -molecule_0_52 0.0 0 A 0.00000000 0.00000000 -molecule_0_53 0.0 0 A 0.00000000 0.00000000 -molecule_0_54 0.0 0 A 0.00000000 0.00000000 -molecule_0_55 0.0 0 A 0.00000000 0.00000000 -molecule_0_56 0.0 0 A 0.00000000 0.00000000 -molecule_0_57 0.0 0 A 0.00000000 0.00000000 -molecule_0_58 0.0 0 A 0.00000000 0.00000000 -molecule_0_59 0.0 0 A 0.00000000 0.00000000 -molecule_0_60 0.0 0 A 0.00000000 0.00000000 -molecule_0_61 0.0 0 A 0.00000000 0.00000000 -molecule_0_62 0.0 0 A 0.00000000 0.00000000 -molecule_0_63 0.0 0 A 0.00000000 0.00000000 -molecule_0_64 0.0 0 A 0.00000000 0.00000000 -molecule_0_65 0.0 0 A 0.00000000 0.00000000 -molecule_0_66 0.0 0 A 0.00000000 0.00000000 -molecule_0_67 0.0 0 A 0.00000000 0.00000000 -molecule_0_68 0.0 0 A 0.00000000 0.00000000 -molecule_0_69 0.0 0 A 0.00000000 0.00000000 -molecule_0_70 0.0 0 A 0.00000000 0.00000000 -molecule_0_71 0.0 0 A 0.00000000 0.00000000 -molecule_0_72 0.0 0 A 0.00000000 0.00000000 -molecule_0_73 0.0 0 A 0.00000000 0.00000000 -molecule_0_74 0.0 0 A 0.00000000 0.00000000 -molecule_0_75 0.0 0 A 0.00000000 0.00000000 -molecule_0_76 0.0 0 A 0.00000000 0.00000000 -molecule_0_77 0.0 0 A 0.00000000 0.00000000 -molecule_0_78 0.0 0 A 0.00000000 0.00000000 -molecule_0_79 0.0 0 A 0.00000000 0.00000000 -molecule_0_80 0.0 0 A 0.00000000 0.00000000 -molecule_0_81 0.0 0 A 0.00000000 0.00000000 -molecule_0_82 0.0 0 A 0.00000000 0.00000000 -molecule_0_83 0.0 0 A 0.00000000 0.00000000 -molecule_0_84 0.0 0 A 0.00000000 0.00000000 -molecule_0_85 0.0 0 A 0.00000000 0.00000000 -molecule_0_86 0.0 0 A 0.00000000 0.00000000 -molecule_0_87 0.0 0 A 0.00000000 0.00000000 -molecule_0_88 0.0 0 A 0.00000000 0.00000000 -molecule_0_89 0.0 0 A 0.00000000 0.00000000 -molecule_0_90 0.0 0 A 0.00000000 0.00000000 -molecule_0_91 0.0 0 A 0.00000000 0.00000000 -molecule_0_92 0.0 0 A 0.00000000 0.00000000 -molecule_0_93 0.0 0 A 0.00000000 0.00000000 -molecule_0_94 0.0 0 A 0.00000000 0.00000000 -molecule_0_95 0.0 0 A 0.00000000 0.00000000 -molecule_0_96 0.0 0 A 0.00000000 0.00000000 -molecule_0_97 0.0 0 A 0.00000000 0.00000000 -molecule_0_98 0.0 0 A 0.00000000 0.00000000 -molecule_0_99 0.0 0 A 0.00000000 0.00000000 -molecule_0_100 0.0 0 A 0.00000000 0.00000000 -molecule_0_101 0.0 0 A 0.00000000 0.00000000 -molecule_0_102 0.0 0 A 0.00000000 0.00000000 -molecule_0_103 0.0 0 A 0.00000000 0.00000000 -molecule_0_104 0.0 0 A 0.00000000 0.00000000 -molecule_0_105 0.0 0 A 0.00000000 0.00000000 -molecule_0_106 0.0 0 A 0.00000000 0.00000000 -molecule_0_107 0.0 0 A 0.00000000 0.00000000 -molecule_0_108 0.0 0 A 0.00000000 0.00000000 -molecule_0_109 0.0 0 A 0.00000000 0.00000000 -molecule_0_110 0.0 0 A 0.00000000 0.00000000 -molecule_0_111 0.0 0 A 0.00000000 0.00000000 -molecule_0_112 0.0 0 A 0.00000000 0.00000000 -molecule_0_113 0.0 0 A 0.00000000 0.00000000 -molecule_0_114 0.0 0 A 0.00000000 0.00000000 -molecule_0_115 0.0 0 A 0.00000000 0.00000000 -molecule_0_116 0.0 0 A 0.00000000 0.00000000 -molecule_0_117 0.0 0 A 0.00000000 0.00000000 -molecule_0_118 0.0 0 A 0.00000000 0.00000000 -molecule_0_119 0.0 0 A 0.00000000 0.00000000 -molecule_0_120 0.0 0 A 0.00000000 0.00000000 -molecule_0_121 0.0 0 A 0.00000000 0.00000000 -molecule_0_122 0.0 0 A 0.00000000 0.00000000 -molecule_0_123 0.0 0 A 0.00000000 0.00000000 -molecule_0_124 0.0 0 A 0.00000000 0.00000000 -molecule_0_125 0.0 0 A 0.00000000 0.00000000 -molecule_0_126 0.0 0 A 0.00000000 0.00000000 -molecule_0_127 0.0 0 A 0.00000000 0.00000000 -molecule_0_128 0.0 0 A 0.00000000 0.00000000 -molecule_0_129 0.0 0 A 0.00000000 0.00000000 +molecule_1 0.0 0 A 0.00000000 0.00000000 +molecule_2 0.0 0 A 0.00000000 0.00000000 +molecule_3 0.0 0 A 0.00000000 0.00000000 +molecule_4 0.0 0 A 0.00000000 0.00000000 +molecule_5 0.0 0 A 0.00000000 0.00000000 +molecule_6 0.0 0 A 0.00000000 0.00000000 +molecule_7 0.0 0 A 0.00000000 0.00000000 +molecule_8 0.0 0 A 0.00000000 0.00000000 +molecule_9 0.0 0 A 0.00000000 0.00000000 +molecule_10 0.0 0 A 0.00000000 0.00000000 +molecule_11 0.0 0 A 0.00000000 0.00000000 +molecule_12 0.0 0 A 0.00000000 0.00000000 +molecule_13 0.0 0 A 0.00000000 0.00000000 +molecule_14 0.0 0 A 0.00000000 0.00000000 +molecule_15 0.0 0 A 0.00000000 0.00000000 +molecule_16 0.0 0 A 0.00000000 0.00000000 +molecule_17 0.0 0 A 0.00000000 0.00000000 +molecule_18 0.0 0 A 0.00000000 0.00000000 +molecule_19 0.0 0 A 0.00000000 0.00000000 +molecule_20 0.0 0 A 0.00000000 0.00000000 +molecule_21 0.0 0 A 0.00000000 0.00000000 +molecule_22 0.0 0 A 0.00000000 0.00000000 +molecule_23 0.0 0 A 0.00000000 0.00000000 +molecule_24 0.0 0 A 0.00000000 0.00000000 +molecule_25 0.0 0 A 0.00000000 0.00000000 +molecule_26 0.0 0 A 0.00000000 0.00000000 +molecule_27 0.0 0 A 0.00000000 0.00000000 +molecule_28 0.0 0 A 0.00000000 0.00000000 +molecule_29 0.0 0 A 0.00000000 0.00000000 +molecule_30 0.0 0 A 0.00000000 0.00000000 +molecule_31 0.0 0 A 0.00000000 0.00000000 +molecule_32 0.0 0 A 0.00000000 0.00000000 +molecule_33 0.0 0 A 0.00000000 0.00000000 +molecule_34 0.0 0 A 0.00000000 0.00000000 +molecule_35 0.0 0 A 0.00000000 0.00000000 +molecule_36 0.0 0 A 0.00000000 0.00000000 +molecule_37 0.0 0 A 0.00000000 0.00000000 +molecule_38 0.0 0 A 0.00000000 0.00000000 +molecule_39 0.0 0 A 0.00000000 0.00000000 +molecule_40 0.0 0 A 0.00000000 0.00000000 +molecule_41 0.0 0 A 0.00000000 0.00000000 +molecule_42 0.0 0 A 0.00000000 0.00000000 +molecule_43 0.0 0 A 0.00000000 0.00000000 +molecule_44 0.0 0 A 0.00000000 0.00000000 +molecule_45 0.0 0 A 0.00000000 0.00000000 +molecule_46 0.0 0 A 0.00000000 0.00000000 +molecule_47 0.0 0 A 0.00000000 0.00000000 +molecule_48 0.0 0 A 0.00000000 0.00000000 +molecule_49 0.0 0 A 0.00000000 0.00000000 +molecule_50 0.0 0 A 0.00000000 0.00000000 +molecule_51 0.0 0 A 0.00000000 0.00000000 +molecule_52 0.0 0 A 0.00000000 0.00000000 +molecule_53 0.0 0 A 0.00000000 0.00000000 +molecule_54 0.0 0 A 0.00000000 0.00000000 +molecule_55 0.0 0 A 0.00000000 0.00000000 +molecule_56 0.0 0 A 0.00000000 0.00000000 +molecule_57 0.0 0 A 0.00000000 0.00000000 +molecule_58 0.0 0 A 0.00000000 0.00000000 +molecule_59 0.0 0 A 0.00000000 0.00000000 +molecule_60 0.0 0 A 0.00000000 0.00000000 +molecule_61 0.0 0 A 0.00000000 0.00000000 +molecule_62 0.0 0 A 0.00000000 0.00000000 +molecule_63 0.0 0 A 0.00000000 0.00000000 +molecule_64 0.0 0 A 0.00000000 0.00000000 +molecule_65 0.0 0 A 0.00000000 0.00000000 +molecule_66 0.0 0 A 0.00000000 0.00000000 +molecule_67 0.0 0 A 0.00000000 0.00000000 +molecule_68 0.0 0 A 0.00000000 0.00000000 +molecule_69 0.0 0 A 0.00000000 0.00000000 +molecule_70 0.0 0 A 0.00000000 0.00000000 +molecule_71 0.0 0 A 0.00000000 0.00000000 +molecule_72 0.0 0 A 0.00000000 0.00000000 +molecule_73 0.0 0 A 0.00000000 0.00000000 +molecule_74 0.0 0 A 0.00000000 0.00000000 +molecule_75 0.0 0 A 0.00000000 0.00000000 +molecule_76 0.0 0 A 0.00000000 0.00000000 +molecule_77 0.0 0 A 0.00000000 0.00000000 +molecule_78 0.0 0 A 0.00000000 0.00000000 +molecule_79 0.0 0 A 0.00000000 0.00000000 +molecule_80 0.0 0 A 0.00000000 0.00000000 +molecule_81 0.0 0 A 0.00000000 0.00000000 +molecule_82 0.0 0 A 0.00000000 0.00000000 +molecule_83 0.0 0 A 0.00000000 0.00000000 +molecule_84 0.0 0 A 0.00000000 0.00000000 +molecule_85 0.0 0 A 0.00000000 0.00000000 +molecule_86 0.0 0 A 0.00000000 0.00000000 +molecule_87 0.0 0 A 0.00000000 0.00000000 +molecule_88 0.0 0 A 0.00000000 0.00000000 +molecule_89 0.0 0 A 0.00000000 0.00000000 +molecule_90 0.0 0 A 0.00000000 0.00000000 +molecule_91 0.0 0 A 0.00000000 0.00000000 +molecule_92 0.0 0 A 0.00000000 0.00000000 +molecule_93 0.0 0 A 0.00000000 0.00000000 +molecule_94 0.0 0 A 0.00000000 0.00000000 +molecule_95 0.0 0 A 0.00000000 0.00000000 +molecule_96 0.0 0 A 0.00000000 0.00000000 +molecule_97 0.0 0 A 0.00000000 0.00000000 +molecule_98 0.0 0 A 0.00000000 0.00000000 +molecule_99 0.0 0 A 0.00000000 0.00000000 +molecule_100 0.0 0 A 0.00000000 0.00000000 +molecule_101 0.0 0 A 0.00000000 0.00000000 +molecule_102 0.0 0 A 0.00000000 0.00000000 +molecule_103 0.0 0 A 0.00000000 0.00000000 +molecule_104 0.0 0 A 0.00000000 0.00000000 +molecule_105 0.0 0 A 0.00000000 0.00000000 +molecule_106 0.0 0 A 0.00000000 0.00000000 +molecule_107 0.0 0 A 0.00000000 0.00000000 +molecule_108 0.0 0 A 0.00000000 0.00000000 +molecule_109 0.0 0 A 0.00000000 0.00000000 +molecule_110 0.0 0 A 0.00000000 0.00000000 +molecule_111 0.0 0 A 0.00000000 0.00000000 +molecule_112 0.0 0 A 0.00000000 0.00000000 +molecule_113 0.0 0 A 0.00000000 0.00000000 +molecule_114 0.0 0 A 0.00000000 0.00000000 +molecule_115 0.0 0 A 0.00000000 0.00000000 +molecule_116 0.0 0 A 0.00000000 0.00000000 +molecule_117 0.0 0 A 0.00000000 0.00000000 +molecule_118 0.0 0 A 0.00000000 0.00000000 +molecule_119 0.0 0 A 0.00000000 0.00000000 +molecule_120 0.0 0 A 0.00000000 0.00000000 +molecule_121 0.0 0 A 0.00000000 0.00000000 +molecule_122 0.0 0 A 0.00000000 0.00000000 +molecule_123 0.0 0 A 0.00000000 0.00000000 +molecule_124 0.0 0 A 0.00000000 0.00000000 +molecule_125 0.0 0 A 0.00000000 0.00000000 +molecule_126 0.0 0 A 0.00000000 0.00000000 +molecule_127 0.0 0 A 0.00000000 0.00000000 +molecule_128 0.0 0 A 0.00000000 0.00000000 +molecule_129 0.0 0 A 0.00000000 0.00000000 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp index 8c545698f..0808f6b09 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp @@ -1,260 +1,260 @@ [ nonbond_params ] -molecule_0_7 molecule_0_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 -molecule_0_8 molecule_0_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 -molecule_0_8 molecule_0_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 -molecule_0_9 molecule_0_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 -molecule_0_10 molecule_0_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 -molecule_0_11 molecule_0_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 -molecule_0_12 molecule_0_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 -molecule_0_13 molecule_0_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 -molecule_0_14 molecule_0_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 -molecule_0_15 molecule_0_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 -molecule_0_16 molecule_0_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 -molecule_0_17 molecule_0_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 -molecule_0_18 molecule_0_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 -molecule_0_20 molecule_0_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 -molecule_0_23 molecule_0_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 -molecule_0_24 molecule_0_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 -molecule_0_24 molecule_0_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 -molecule_0_25 molecule_0_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 -molecule_0_25 molecule_0_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 -molecule_0_25 molecule_0_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 -molecule_0_25 molecule_0_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 -molecule_0_27 molecule_0_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 -molecule_0_27 molecule_0_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 -molecule_0_28 molecule_0_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 -molecule_0_28 molecule_0_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 -molecule_0_28 molecule_0_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 -molecule_0_28 molecule_0_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 -molecule_0_29 molecule_0_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 -molecule_0_29 molecule_0_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 -molecule_0_29 molecule_0_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 -molecule_0_29 molecule_0_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 -molecule_0_30 molecule_0_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 -molecule_0_31 molecule_0_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 -molecule_0_32 molecule_0_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 -molecule_0_32 molecule_0_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 -molecule_0_33 molecule_0_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 -molecule_0_34 molecule_0_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 -molecule_0_35 molecule_0_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 -molecule_0_36 molecule_0_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 -molecule_0_37 molecule_0_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 -molecule_0_37 molecule_0_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 -molecule_0_38 molecule_0_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 -molecule_0_38 molecule_0_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 -molecule_0_38 molecule_0_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 -molecule_0_38 molecule_0_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 -molecule_0_38 molecule_0_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 -molecule_0_38 molecule_0_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 -molecule_0_38 molecule_0_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 -molecule_0_38 molecule_0_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 -molecule_0_39 molecule_0_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 -molecule_0_39 molecule_0_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 -molecule_0_40 molecule_0_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 -molecule_0_40 molecule_0_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 -molecule_0_41 molecule_0_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 -molecule_0_42 molecule_0_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 -molecule_0_44 molecule_0_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 -molecule_0_49 molecule_0_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 -molecule_0_50 molecule_0_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 -molecule_0_50 molecule_0_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 -molecule_0_51 molecule_0_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 -molecule_0_51 molecule_0_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 -molecule_0_51 molecule_0_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 -molecule_0_51 molecule_0_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 -molecule_0_52 molecule_0_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 -molecule_0_52 molecule_0_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 -molecule_0_52 molecule_0_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 -molecule_0_53 molecule_0_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 -molecule_0_53 molecule_0_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 -molecule_0_54 molecule_0_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 -molecule_0_54 molecule_0_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 -molecule_0_54 molecule_0_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 -molecule_0_55 molecule_0_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 -molecule_0_55 molecule_0_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 -molecule_0_55 molecule_0_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 -molecule_0_55 molecule_0_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 -molecule_0_55 molecule_0_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 -molecule_0_55 molecule_0_38 1 0.53863592 9.41400000 ;go bond 0.6045983765957093 -molecule_0_55 molecule_0_39 1 0.46884965 9.41400000 ;go bond 0.5262659343028784 -molecule_0_55 molecule_0_40 1 0.49397051 9.41400000 ;go bond 0.5544631488965023 -molecule_0_56 molecule_0_31 1 0.63305577 9.41400000 ;go bond 0.7105810801311345 -molecule_0_56 molecule_0_32 1 0.57070473 9.41400000 ;go bond 0.6405943964432239 -molecule_0_56 molecule_0_35 1 0.54499611 9.41400000 ;go bond 0.6117374504966917 -molecule_0_57 molecule_0_35 1 0.59142457 9.41400000 ;go bond 0.6638516326030536 -molecule_0_57 molecule_0_36 1 0.73443635 9.41400000 ;go bond 0.8243769340599911 -molecule_0_57 molecule_0_42 1 0.68123116 9.41400000 ;go bond 0.7646561231921536 -molecule_0_57 molecule_0_43 1 0.72932038 9.41400000 ;go bond 0.8186344517277264 -molecule_0_57 molecule_0_44 1 0.71017360 9.41400000 ;go bond 0.7971429108051539 -molecule_0_57 molecule_0_52 1 0.45255106 9.41400000 ;go bond 0.5079713907835711 -molecule_0_57 molecule_0_53 1 0.35572883 9.41400000 ;go bond 0.3992921109620664 -molecule_0_58 molecule_0_52 1 0.41486867 9.41400000 ;go bond 0.4656743363160884 -molecule_0_58 molecule_0_53 1 0.33528745 9.41400000 ;go bond 0.37634743770658646 -molecule_0_59 molecule_0_46 1 0.92985190 9.41400000 ;go bond 1.0437234628284975 -molecule_0_59 molecule_0_50 1 0.67865311 9.41400000 ;go bond 0.7617623567683692 -molecule_0_59 molecule_0_51 1 0.46599015 9.41400000 ;go bond 0.5230562584392384 -molecule_0_59 molecule_0_52 1 0.52411606 9.41400000 ;go bond 0.5883003833904864 -molecule_0_60 molecule_0_50 1 0.55757626 9.41400000 ;go bond 0.6258581889054639 -molecule_0_60 molecule_0_51 1 0.45353930 9.41400000 ;go bond 0.5090806492037284 -molecule_0_60 molecule_0_53 1 0.78554721 9.41400000 ;go bond 0.8817469319963909 -molecule_0_61 molecule_0_48 1 0.83253174 9.41400000 ;go bond 0.9344852838875899 -molecule_0_61 molecule_0_50 1 0.65515556 9.41400000 ;go bond 0.7353872567523113 -molecule_0_63 molecule_0_58 1 0.62967119 9.41400000 ;go bond 0.7067820082223201 -molecule_0_63 molecule_0_59 1 0.46427561 9.41400000 ;go bond 0.521131754230626 -molecule_0_64 molecule_0_53 1 0.82959737 9.41400000 ;go bond 0.9311915604701376 -molecule_0_64 molecule_0_60 1 0.38156281 9.41400000 ;go bond 0.4282897748904594 -molecule_0_66 molecule_0_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 -molecule_0_66 molecule_0_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 -molecule_0_68 molecule_0_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 -molecule_0_69 molecule_0_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 -molecule_0_69 molecule_0_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 -molecule_0_69 molecule_0_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 -molecule_0_69 molecule_0_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 -molecule_0_70 molecule_0_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 -molecule_0_72 molecule_0_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 -molecule_0_72 molecule_0_61 1 0.44682674 9.41400000 ;go bond 0.5015460538054222 -molecule_0_72 molecule_0_64 1 0.62949829 9.41400000 ;go bond 0.7065879353028186 -molecule_0_73 molecule_0_61 1 0.53130673 9.41400000 ;go bond 0.5963716385459682 -molecule_0_73 molecule_0_62 1 0.40729971 9.41400000 ;go bond 0.4571784705977002 -molecule_0_74 molecule_0_62 1 0.44897571 9.41400000 ;go bond 0.5039581950921611 -molecule_0_74 molecule_0_63 1 0.38506256 9.41400000 ;go bond 0.43221810950469636 -molecule_0_74 molecule_0_64 1 0.43052761 9.41400000 ;go bond 0.4832509069633833 -molecule_0_74 molecule_0_65 1 0.61184241 9.41400000 ;go bond 0.6867698876930867 -molecule_0_75 molecule_0_62 1 0.52199782 9.41400000 ;go bond 0.5859227452973559 -molecule_0_75 molecule_0_63 1 0.40610455 9.41400000 ;go bond 0.45583694740556885 -molecule_0_76 molecule_0_63 1 0.46409225 9.41400000 ;go bond 0.5209259369461889 -molecule_0_78 molecule_0_63 1 0.57576077 9.41400000 ;go bond 0.6462696105707938 -molecule_0_78 molecule_0_64 1 0.45724502 9.41400000 ;go bond 0.5132401787770625 -molecule_0_78 molecule_0_65 1 0.43974215 9.41400000 ;go bond 0.4935938729629976 -molecule_0_78 molecule_0_74 1 0.56052614 9.41400000 ;go bond 0.6291693208239874 -molecule_0_79 molecule_0_64 1 0.52803406 9.41400000 ;go bond 0.5926981930678074 -molecule_0_79 molecule_0_65 1 0.39916015 9.41400000 ;go bond 0.44804212253596193 -molecule_0_80 molecule_0_53 1 0.60673469 9.41400000 ;go bond 0.6810366626079589 -molecule_0_80 molecule_0_60 1 0.73868742 9.41400000 ;go bond 0.8291485950674535 -molecule_0_80 molecule_0_64 1 0.54789421 9.41400000 ;go bond 0.6149904606975389 -molecule_0_80 molecule_0_65 1 0.47057069 9.41400000 ;go bond 0.5281977457102484 -molecule_0_80 molecule_0_66 1 0.58883652 9.41400000 ;go bond 0.6609466408239479 -molecule_0_82 molecule_0_78 1 0.66632073 9.41400000 ;go bond 0.7479197331826131 -molecule_0_83 molecule_0_53 1 0.51788905 9.41400000 ;go bond 0.581310806103053 -molecule_0_83 molecule_0_54 1 0.51088855 9.41400000 ;go bond 0.5734530137551908 -molecule_0_83 molecule_0_58 1 0.70980394 9.41400000 ;go bond 0.7967279839859979 -molecule_0_83 molecule_0_64 1 0.89499397 9.41400000 ;go bond 1.0045967605887745 -molecule_0_83 molecule_0_78 1 0.81556181 9.41400000 ;go bond 0.9154371804917103 -molecule_0_84 molecule_0_40 1 0.40226578 9.41400000 ;go bond 0.45152806893595954 -molecule_0_84 molecule_0_41 1 0.48796771 9.41400000 ;go bond 0.5477252325235119 -molecule_0_84 molecule_0_42 1 0.63252675 9.41400000 ;go bond 0.7099872721863867 -molecule_0_84 molecule_0_43 1 0.89270990 9.41400000 ;go bond 1.0020329775751635 -molecule_0_84 molecule_0_53 1 0.66502200 9.41400000 ;go bond 0.7464619538686407 -molecule_0_84 molecule_0_54 1 0.56665258 9.41400000 ;go bond 0.6360460147186728 -molecule_0_85 molecule_0_40 1 0.48170210 9.41400000 ;go bond 0.5406923273735796 -molecule_0_85 molecule_0_81 1 0.64785523 9.41400000 ;go bond 0.7271929039256984 -molecule_0_86 molecule_0_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 -molecule_0_86 molecule_0_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 -molecule_0_86 molecule_0_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 -molecule_0_88 molecule_0_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 -molecule_0_88 molecule_0_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 -molecule_0_88 molecule_0_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 -molecule_0_88 molecule_0_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 -molecule_0_88 molecule_0_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 -molecule_0_88 molecule_0_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 -molecule_0_89 molecule_0_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 -molecule_0_89 molecule_0_15 1 0.69215886 9.41400000 ;go bond 0.7769220558398894 -molecule_0_90 molecule_0_78 1 0.80563795 9.41400000 ;go bond 0.9042980239792853 -molecule_0_90 molecule_0_82 1 0.59740893 9.41400000 ;go bond 0.6705688513824994 -molecule_0_90 molecule_0_83 1 0.57714934 9.41400000 ;go bond 0.6478282257424317 -molecule_0_91 molecule_0_55 1 0.70847337 9.41400000 ;go bond 0.7952344695348353 -molecule_0_91 molecule_0_58 1 0.76773720 9.41400000 ;go bond 0.8617558647944001 -molecule_0_91 molecule_0_83 1 0.57795007 9.41400000 ;go bond 0.6487270215620753 -molecule_0_92 molecule_0_15 1 0.66057405 9.41400000 ;go bond 0.741469302181026 -molecule_0_92 molecule_0_17 1 0.76276340 9.41400000 ;go bond 0.8561729710147924 -molecule_0_92 molecule_0_88 1 0.55891711 9.41400000 ;go bond 0.6273632448163519 -molecule_0_93 molecule_0_89 1 0.55091233 9.41400000 ;go bond 0.6183781864423775 -molecule_0_94 molecule_0_58 1 0.80192436 9.41400000 ;go bond 0.9001296640477775 -molecule_0_94 molecule_0_63 1 0.69400655 9.41400000 ;go bond 0.7789960144450432 -molecule_0_94 molecule_0_76 1 0.58706169 9.41400000 ;go bond 0.6589544684537765 -molecule_0_94 molecule_0_78 1 0.87593032 9.41400000 ;go bond 0.9831985419578763 -molecule_0_94 molecule_0_83 1 0.89829847 9.41400000 ;go bond 1.0083059444227724 -molecule_0_94 molecule_0_90 1 0.53696870 9.41400000 ;go bond 0.6027269866522963 -molecule_0_95 molecule_0_28 1 0.94028879 9.41400000 ;go bond 1.0554384813372668 -molecule_0_95 molecule_0_56 1 0.76727508 9.41400000 ;go bond 0.8612371596953154 -molecule_0_95 molecule_0_58 1 0.83998475 9.41400000 ;go bond 0.9428510053550558 -molecule_0_95 molecule_0_91 1 0.53148309 9.41400000 ;go bond 0.5965695928114466 -molecule_0_96 molecule_0_15 1 0.94537258 9.41400000 ;go bond 1.0611448446580265 -molecule_0_96 molecule_0_16 1 0.84805127 9.41400000 ;go bond 0.9519053644995195 -molecule_0_96 molecule_0_17 1 0.81454872 9.41400000 ;go bond 0.9143000281459933 -molecule_0_96 molecule_0_20 1 0.73587759 9.41400000 ;go bond 0.8259946673768416 -molecule_0_96 molecule_0_92 1 0.54860993 9.41400000 ;go bond 0.6157938252917854 -molecule_0_97 molecule_0_63 1 0.84557275 9.41400000 ;go bond 0.9491233248865086 -molecule_0_97 molecule_0_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 -molecule_0_97 molecule_0_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 -molecule_0_98 molecule_0_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 -molecule_0_98 molecule_0_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 -molecule_0_98 molecule_0_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 -molecule_0_99 molecule_0_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 -molecule_0_99 molecule_0_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 -molecule_0_99 molecule_0_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 -molecule_0_99 molecule_0_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 -molecule_0_100 molecule_0_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 -molecule_0_100 molecule_0_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 -molecule_0_100 molecule_0_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 -molecule_0_101 molecule_0_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 -molecule_0_104 molecule_0_23 1 0.90496194 9.41400000 ;go bond 1.0157854279713863 -molecule_0_104 molecule_0_99 1 0.37779975 9.41400000 ;go bond 0.42406587714866395 -molecule_0_105 molecule_0_23 1 0.85792539 9.41400000 ;go bond 0.9629886926477136 -molecule_0_105 molecule_0_27 1 0.80028132 9.41400000 ;go bond 0.8982854095190085 -molecule_0_105 molecule_0_28 1 0.85914649 9.41400000 ;go bond 0.9643593287596212 -molecule_0_105 molecule_0_31 1 0.84674626 9.41400000 ;go bond 0.950440544780807 -molecule_0_105 molecule_0_99 1 0.58741430 9.41400000 ;go bond 0.6593502594081683 -molecule_0_107 molecule_0_98 1 0.70183885 9.41400000 ;go bond 0.7877874714268905 -molecule_0_108 molecule_0_28 1 0.92956079 9.41400000 ;go bond 1.0433967044744268 -molecule_0_108 molecule_0_35 1 0.82960839 9.41400000 ;go bond 0.9312039368635526 -molecule_0_108 molecule_0_56 1 0.78133210 9.41400000 ;go bond 0.8770156294387439 -molecule_0_108 molecule_0_57 1 0.77168204 9.41400000 ;go bond 0.8661838041857776 -molecule_0_108 molecule_0_98 1 0.90403083 9.41400000 ;go bond 1.014740292066367 -molecule_0_108 molecule_0_99 1 0.90315750 9.41400000 ;go bond 1.0137600206889819 -molecule_0_110 molecule_0_34 1 0.54869664 9.41400000 ;go bond 0.6158911542488904 -molecule_0_110 molecule_0_35 1 0.64980269 9.41400000 ;go bond 0.7293788607697123 -molecule_0_111 molecule_0_27 1 0.70311941 9.41400000 ;go bond 0.7892248529963473 -molecule_0_111 molecule_0_31 1 0.56259884 9.41400000 ;go bond 0.6314958500157425 -molecule_0_111 molecule_0_105 1 0.59346888 9.41400000 ;go bond 0.6661462995266982 -molecule_0_111 molecule_0_106 1 0.59882239 9.41400000 ;go bond 0.6721554100763635 -molecule_0_112 molecule_0_106 1 0.57753815 9.41400000 ;go bond 0.6482646568405853 -molecule_0_112 molecule_0_107 1 0.74260248 9.41400000 ;go bond 0.833543103918769 -molecule_0_112 molecule_0_108 1 0.53753958 9.41400000 ;go bond 0.603367775987529 -molecule_0_113 molecule_0_109 1 0.53306219 9.41400000 ;go bond 0.5983420831461288 -molecule_0_114 molecule_0_34 1 0.72771145 9.41400000 ;go bond 0.8168284821715603 -molecule_0_114 molecule_0_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 -molecule_0_115 molecule_0_30 1 0.62277169 9.41400000 ;go bond 0.6990375917289473 -molecule_0_115 molecule_0_31 1 0.71820218 9.41400000 ;go bond 0.8061546928175227 -molecule_0_115 molecule_0_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 -molecule_0_115 molecule_0_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 -molecule_0_115 molecule_0_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 -molecule_0_116 molecule_0_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 -molecule_0_116 molecule_0_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 -molecule_0_116 molecule_0_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 -molecule_0_118 molecule_0_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 -molecule_0_120 molecule_0_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 -molecule_0_120 molecule_0_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 -molecule_0_120 molecule_0_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 -molecule_0_120 molecule_0_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 -molecule_0_120 molecule_0_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 -molecule_0_122 molecule_0_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 -molecule_0_123 molecule_0_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 -molecule_0_123 molecule_0_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 -molecule_0_123 molecule_0_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 -molecule_0_123 molecule_0_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 -molecule_0_123 molecule_0_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 -molecule_0_123 molecule_0_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 -molecule_0_124 molecule_0_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 -molecule_0_124 molecule_0_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 -molecule_0_124 molecule_0_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 -molecule_0_124 molecule_0_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 -molecule_0_124 molecule_0_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 -molecule_0_125 molecule_0_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 -molecule_0_125 molecule_0_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 -molecule_0_127 molecule_0_5 1 0.79805432 9.41400000 ;go bond 0.8957856911439042 -molecule_0_127 molecule_0_6 1 0.59870073 9.41400000 ;go bond 0.6720188457372778 -molecule_0_129 molecule_0_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 -molecule_0_129 molecule_0_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 -molecule_0_129 molecule_0_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 -molecule_0_129 molecule_0_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 +molecule_7 molecule_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 +molecule_8 molecule_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 +molecule_8 molecule_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 +molecule_9 molecule_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 +molecule_10 molecule_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 +molecule_11 molecule_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 +molecule_12 molecule_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 +molecule_13 molecule_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 +molecule_14 molecule_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 +molecule_15 molecule_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 +molecule_16 molecule_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 +molecule_17 molecule_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 +molecule_18 molecule_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 +molecule_20 molecule_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 +molecule_23 molecule_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 +molecule_24 molecule_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 +molecule_24 molecule_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 +molecule_25 molecule_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 +molecule_25 molecule_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 +molecule_25 molecule_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 +molecule_25 molecule_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 +molecule_27 molecule_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 +molecule_27 molecule_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 +molecule_28 molecule_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 +molecule_28 molecule_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 +molecule_28 molecule_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 +molecule_28 molecule_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 +molecule_29 molecule_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 +molecule_29 molecule_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 +molecule_29 molecule_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 +molecule_29 molecule_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 +molecule_30 molecule_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 +molecule_31 molecule_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 +molecule_32 molecule_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 +molecule_32 molecule_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 +molecule_33 molecule_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 +molecule_34 molecule_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 +molecule_35 molecule_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 +molecule_36 molecule_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 +molecule_37 molecule_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 +molecule_37 molecule_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 +molecule_38 molecule_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 +molecule_38 molecule_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 +molecule_38 molecule_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 +molecule_38 molecule_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 +molecule_38 molecule_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 +molecule_38 molecule_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 +molecule_38 molecule_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 +molecule_38 molecule_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 +molecule_39 molecule_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 +molecule_39 molecule_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 +molecule_40 molecule_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 +molecule_40 molecule_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 +molecule_41 molecule_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 +molecule_42 molecule_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 +molecule_44 molecule_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 +molecule_49 molecule_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 +molecule_50 molecule_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 +molecule_50 molecule_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 +molecule_51 molecule_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 +molecule_51 molecule_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 +molecule_51 molecule_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 +molecule_51 molecule_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 +molecule_52 molecule_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 +molecule_52 molecule_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 +molecule_52 molecule_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 +molecule_53 molecule_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 +molecule_53 molecule_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 +molecule_54 molecule_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 +molecule_54 molecule_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 +molecule_54 molecule_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 +molecule_55 molecule_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 +molecule_55 molecule_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 +molecule_55 molecule_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 +molecule_55 molecule_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 +molecule_55 molecule_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 +molecule_55 molecule_38 1 0.53863592 9.41400000 ;go bond 0.6045983765957093 +molecule_55 molecule_39 1 0.46884965 9.41400000 ;go bond 0.5262659343028784 +molecule_55 molecule_40 1 0.49397051 9.41400000 ;go bond 0.5544631488965023 +molecule_56 molecule_31 1 0.63305577 9.41400000 ;go bond 0.7105810801311345 +molecule_56 molecule_32 1 0.57070473 9.41400000 ;go bond 0.6405943964432239 +molecule_56 molecule_35 1 0.54499611 9.41400000 ;go bond 0.6117374504966917 +molecule_57 molecule_35 1 0.59142457 9.41400000 ;go bond 0.6638516326030536 +molecule_57 molecule_36 1 0.73443635 9.41400000 ;go bond 0.8243769340599911 +molecule_57 molecule_42 1 0.68123116 9.41400000 ;go bond 0.7646561231921536 +molecule_57 molecule_43 1 0.72932038 9.41400000 ;go bond 0.8186344517277264 +molecule_57 molecule_44 1 0.71017360 9.41400000 ;go bond 0.7971429108051539 +molecule_57 molecule_52 1 0.45255106 9.41400000 ;go bond 0.5079713907835711 +molecule_57 molecule_53 1 0.35572883 9.41400000 ;go bond 0.3992921109620664 +molecule_58 molecule_52 1 0.41486867 9.41400000 ;go bond 0.4656743363160884 +molecule_58 molecule_53 1 0.33528745 9.41400000 ;go bond 0.37634743770658646 +molecule_59 molecule_46 1 0.92985190 9.41400000 ;go bond 1.0437234628284975 +molecule_59 molecule_50 1 0.67865311 9.41400000 ;go bond 0.7617623567683692 +molecule_59 molecule_51 1 0.46599015 9.41400000 ;go bond 0.5230562584392384 +molecule_59 molecule_52 1 0.52411606 9.41400000 ;go bond 0.5883003833904864 +molecule_60 molecule_50 1 0.55757626 9.41400000 ;go bond 0.6258581889054639 +molecule_60 molecule_51 1 0.45353930 9.41400000 ;go bond 0.5090806492037284 +molecule_60 molecule_53 1 0.78554721 9.41400000 ;go bond 0.8817469319963909 +molecule_61 molecule_48 1 0.83253174 9.41400000 ;go bond 0.9344852838875899 +molecule_61 molecule_50 1 0.65515556 9.41400000 ;go bond 0.7353872567523113 +molecule_63 molecule_58 1 0.62967119 9.41400000 ;go bond 0.7067820082223201 +molecule_63 molecule_59 1 0.46427561 9.41400000 ;go bond 0.521131754230626 +molecule_64 molecule_53 1 0.82959737 9.41400000 ;go bond 0.9311915604701376 +molecule_64 molecule_60 1 0.38156281 9.41400000 ;go bond 0.4282897748904594 +molecule_66 molecule_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 +molecule_66 molecule_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 +molecule_68 molecule_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 +molecule_69 molecule_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 +molecule_69 molecule_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 +molecule_69 molecule_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 +molecule_69 molecule_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 +molecule_70 molecule_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 +molecule_72 molecule_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 +molecule_72 molecule_61 1 0.44682674 9.41400000 ;go bond 0.5015460538054222 +molecule_72 molecule_64 1 0.62949829 9.41400000 ;go bond 0.7065879353028186 +molecule_73 molecule_61 1 0.53130673 9.41400000 ;go bond 0.5963716385459682 +molecule_73 molecule_62 1 0.40729971 9.41400000 ;go bond 0.4571784705977002 +molecule_74 molecule_62 1 0.44897571 9.41400000 ;go bond 0.5039581950921611 +molecule_74 molecule_63 1 0.38506256 9.41400000 ;go bond 0.43221810950469636 +molecule_74 molecule_64 1 0.43052761 9.41400000 ;go bond 0.4832509069633833 +molecule_74 molecule_65 1 0.61184241 9.41400000 ;go bond 0.6867698876930867 +molecule_75 molecule_62 1 0.52199782 9.41400000 ;go bond 0.5859227452973559 +molecule_75 molecule_63 1 0.40610455 9.41400000 ;go bond 0.45583694740556885 +molecule_76 molecule_63 1 0.46409225 9.41400000 ;go bond 0.5209259369461889 +molecule_78 molecule_63 1 0.57576077 9.41400000 ;go bond 0.6462696105707938 +molecule_78 molecule_64 1 0.45724502 9.41400000 ;go bond 0.5132401787770625 +molecule_78 molecule_65 1 0.43974215 9.41400000 ;go bond 0.4935938729629976 +molecule_78 molecule_74 1 0.56052614 9.41400000 ;go bond 0.6291693208239874 +molecule_79 molecule_64 1 0.52803406 9.41400000 ;go bond 0.5926981930678074 +molecule_79 molecule_65 1 0.39916015 9.41400000 ;go bond 0.44804212253596193 +molecule_80 molecule_53 1 0.60673469 9.41400000 ;go bond 0.6810366626079589 +molecule_80 molecule_60 1 0.73868742 9.41400000 ;go bond 0.8291485950674535 +molecule_80 molecule_64 1 0.54789421 9.41400000 ;go bond 0.6149904606975389 +molecule_80 molecule_65 1 0.47057069 9.41400000 ;go bond 0.5281977457102484 +molecule_80 molecule_66 1 0.58883652 9.41400000 ;go bond 0.6609466408239479 +molecule_82 molecule_78 1 0.66632073 9.41400000 ;go bond 0.7479197331826131 +molecule_83 molecule_53 1 0.51788905 9.41400000 ;go bond 0.581310806103053 +molecule_83 molecule_54 1 0.51088855 9.41400000 ;go bond 0.5734530137551908 +molecule_83 molecule_58 1 0.70980394 9.41400000 ;go bond 0.7967279839859979 +molecule_83 molecule_64 1 0.89499397 9.41400000 ;go bond 1.0045967605887745 +molecule_83 molecule_78 1 0.81556181 9.41400000 ;go bond 0.9154371804917103 +molecule_84 molecule_40 1 0.40226578 9.41400000 ;go bond 0.45152806893595954 +molecule_84 molecule_41 1 0.48796771 9.41400000 ;go bond 0.5477252325235119 +molecule_84 molecule_42 1 0.63252675 9.41400000 ;go bond 0.7099872721863867 +molecule_84 molecule_43 1 0.89270990 9.41400000 ;go bond 1.0020329775751635 +molecule_84 molecule_53 1 0.66502200 9.41400000 ;go bond 0.7464619538686407 +molecule_84 molecule_54 1 0.56665258 9.41400000 ;go bond 0.6360460147186728 +molecule_85 molecule_40 1 0.48170210 9.41400000 ;go bond 0.5406923273735796 +molecule_85 molecule_81 1 0.64785523 9.41400000 ;go bond 0.7271929039256984 +molecule_86 molecule_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 +molecule_86 molecule_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 +molecule_86 molecule_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 +molecule_88 molecule_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 +molecule_88 molecule_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 +molecule_88 molecule_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 +molecule_88 molecule_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 +molecule_88 molecule_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 +molecule_88 molecule_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 +molecule_89 molecule_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 +molecule_89 molecule_15 1 0.69215886 9.41400000 ;go bond 0.7769220558398894 +molecule_90 molecule_78 1 0.80563795 9.41400000 ;go bond 0.9042980239792853 +molecule_90 molecule_82 1 0.59740893 9.41400000 ;go bond 0.6705688513824994 +molecule_90 molecule_83 1 0.57714934 9.41400000 ;go bond 0.6478282257424317 +molecule_91 molecule_55 1 0.70847337 9.41400000 ;go bond 0.7952344695348353 +molecule_91 molecule_58 1 0.76773720 9.41400000 ;go bond 0.8617558647944001 +molecule_91 molecule_83 1 0.57795007 9.41400000 ;go bond 0.6487270215620753 +molecule_92 molecule_15 1 0.66057405 9.41400000 ;go bond 0.741469302181026 +molecule_92 molecule_17 1 0.76276340 9.41400000 ;go bond 0.8561729710147924 +molecule_92 molecule_88 1 0.55891711 9.41400000 ;go bond 0.6273632448163519 +molecule_93 molecule_89 1 0.55091233 9.41400000 ;go bond 0.6183781864423775 +molecule_94 molecule_58 1 0.80192436 9.41400000 ;go bond 0.9001296640477775 +molecule_94 molecule_63 1 0.69400655 9.41400000 ;go bond 0.7789960144450432 +molecule_94 molecule_76 1 0.58706169 9.41400000 ;go bond 0.6589544684537765 +molecule_94 molecule_78 1 0.87593032 9.41400000 ;go bond 0.9831985419578763 +molecule_94 molecule_83 1 0.89829847 9.41400000 ;go bond 1.0083059444227724 +molecule_94 molecule_90 1 0.53696870 9.41400000 ;go bond 0.6027269866522963 +molecule_95 molecule_28 1 0.94028879 9.41400000 ;go bond 1.0554384813372668 +molecule_95 molecule_56 1 0.76727508 9.41400000 ;go bond 0.8612371596953154 +molecule_95 molecule_58 1 0.83998475 9.41400000 ;go bond 0.9428510053550558 +molecule_95 molecule_91 1 0.53148309 9.41400000 ;go bond 0.5965695928114466 +molecule_96 molecule_15 1 0.94537258 9.41400000 ;go bond 1.0611448446580265 +molecule_96 molecule_16 1 0.84805127 9.41400000 ;go bond 0.9519053644995195 +molecule_96 molecule_17 1 0.81454872 9.41400000 ;go bond 0.9143000281459933 +molecule_96 molecule_20 1 0.73587759 9.41400000 ;go bond 0.8259946673768416 +molecule_96 molecule_92 1 0.54860993 9.41400000 ;go bond 0.6157938252917854 +molecule_97 molecule_63 1 0.84557275 9.41400000 ;go bond 0.9491233248865086 +molecule_97 molecule_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 +molecule_97 molecule_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 +molecule_98 molecule_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 +molecule_98 molecule_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 +molecule_98 molecule_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 +molecule_99 molecule_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 +molecule_99 molecule_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 +molecule_99 molecule_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 +molecule_99 molecule_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 +molecule_100 molecule_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 +molecule_100 molecule_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 +molecule_100 molecule_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 +molecule_101 molecule_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 +molecule_104 molecule_23 1 0.90496194 9.41400000 ;go bond 1.0157854279713863 +molecule_104 molecule_99 1 0.37779975 9.41400000 ;go bond 0.42406587714866395 +molecule_105 molecule_23 1 0.85792539 9.41400000 ;go bond 0.9629886926477136 +molecule_105 molecule_27 1 0.80028132 9.41400000 ;go bond 0.8982854095190085 +molecule_105 molecule_28 1 0.85914649 9.41400000 ;go bond 0.9643593287596212 +molecule_105 molecule_31 1 0.84674626 9.41400000 ;go bond 0.950440544780807 +molecule_105 molecule_99 1 0.58741430 9.41400000 ;go bond 0.6593502594081683 +molecule_107 molecule_98 1 0.70183885 9.41400000 ;go bond 0.7877874714268905 +molecule_108 molecule_28 1 0.92956079 9.41400000 ;go bond 1.0433967044744268 +molecule_108 molecule_35 1 0.82960839 9.41400000 ;go bond 0.9312039368635526 +molecule_108 molecule_56 1 0.78133210 9.41400000 ;go bond 0.8770156294387439 +molecule_108 molecule_57 1 0.77168204 9.41400000 ;go bond 0.8661838041857776 +molecule_108 molecule_98 1 0.90403083 9.41400000 ;go bond 1.014740292066367 +molecule_108 molecule_99 1 0.90315750 9.41400000 ;go bond 1.0137600206889819 +molecule_110 molecule_34 1 0.54869664 9.41400000 ;go bond 0.6158911542488904 +molecule_110 molecule_35 1 0.64980269 9.41400000 ;go bond 0.7293788607697123 +molecule_111 molecule_27 1 0.70311941 9.41400000 ;go bond 0.7892248529963473 +molecule_111 molecule_31 1 0.56259884 9.41400000 ;go bond 0.6314958500157425 +molecule_111 molecule_105 1 0.59346888 9.41400000 ;go bond 0.6661462995266982 +molecule_111 molecule_106 1 0.59882239 9.41400000 ;go bond 0.6721554100763635 +molecule_112 molecule_106 1 0.57753815 9.41400000 ;go bond 0.6482646568405853 +molecule_112 molecule_107 1 0.74260248 9.41400000 ;go bond 0.833543103918769 +molecule_112 molecule_108 1 0.53753958 9.41400000 ;go bond 0.603367775987529 +molecule_113 molecule_109 1 0.53306219 9.41400000 ;go bond 0.5983420831461288 +molecule_114 molecule_34 1 0.72771145 9.41400000 ;go bond 0.8168284821715603 +molecule_114 molecule_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 +molecule_115 molecule_30 1 0.62277169 9.41400000 ;go bond 0.6990375917289473 +molecule_115 molecule_31 1 0.71820218 9.41400000 ;go bond 0.8061546928175227 +molecule_115 molecule_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 +molecule_115 molecule_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 +molecule_115 molecule_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 +molecule_116 molecule_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 +molecule_116 molecule_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 +molecule_116 molecule_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 +molecule_118 molecule_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 +molecule_120 molecule_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 +molecule_120 molecule_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 +molecule_120 molecule_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 +molecule_120 molecule_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 +molecule_120 molecule_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 +molecule_122 molecule_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 +molecule_123 molecule_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 +molecule_123 molecule_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 +molecule_123 molecule_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 +molecule_123 molecule_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 +molecule_123 molecule_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 +molecule_123 molecule_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 +molecule_124 molecule_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 +molecule_124 molecule_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 +molecule_124 molecule_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 +molecule_124 molecule_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 +molecule_124 molecule_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 +molecule_125 molecule_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 +molecule_125 molecule_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 +molecule_127 molecule_5 1 0.79805432 9.41400000 ;go bond 0.8957856911439042 +molecule_127 molecule_6 1 0.59870073 9.41400000 ;go bond 0.6720188457372778 +molecule_129 molecule_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 +molecule_129 molecule_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 +molecule_129 molecule_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 +molecule_129 molecule_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp index bcbcf6145..3b028c477 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp @@ -1,130 +1,130 @@ [ atomtypes ] -molecule_0_1 0.0 0 A 0.00000000 0.00000000 -molecule_0_2 0.0 0 A 0.00000000 0.00000000 -molecule_0_3 0.0 0 A 0.00000000 0.00000000 -molecule_0_4 0.0 0 A 0.00000000 0.00000000 -molecule_0_5 0.0 0 A 0.00000000 0.00000000 -molecule_0_6 0.0 0 A 0.00000000 0.00000000 -molecule_0_7 0.0 0 A 0.00000000 0.00000000 -molecule_0_8 0.0 0 A 0.00000000 0.00000000 -molecule_0_9 0.0 0 A 0.00000000 0.00000000 -molecule_0_10 0.0 0 A 0.00000000 0.00000000 -molecule_0_11 0.0 0 A 0.00000000 0.00000000 -molecule_0_12 0.0 0 A 0.00000000 0.00000000 -molecule_0_13 0.0 0 A 0.00000000 0.00000000 -molecule_0_14 0.0 0 A 0.00000000 0.00000000 -molecule_0_15 0.0 0 A 0.00000000 0.00000000 -molecule_0_16 0.0 0 A 0.00000000 0.00000000 -molecule_0_17 0.0 0 A 0.00000000 0.00000000 -molecule_0_18 0.0 0 A 0.00000000 0.00000000 -molecule_0_19 0.0 0 A 0.00000000 0.00000000 -molecule_0_20 0.0 0 A 0.00000000 0.00000000 -molecule_0_21 0.0 0 A 0.00000000 0.00000000 -molecule_0_22 0.0 0 A 0.00000000 0.00000000 -molecule_0_23 0.0 0 A 0.00000000 0.00000000 -molecule_0_24 0.0 0 A 0.00000000 0.00000000 -molecule_0_25 0.0 0 A 0.00000000 0.00000000 -molecule_0_26 0.0 0 A 0.00000000 0.00000000 -molecule_0_27 0.0 0 A 0.00000000 0.00000000 -molecule_0_28 0.0 0 A 0.00000000 0.00000000 -molecule_0_29 0.0 0 A 0.00000000 0.00000000 -molecule_0_30 0.0 0 A 0.00000000 0.00000000 -molecule_0_31 0.0 0 A 0.00000000 0.00000000 -molecule_0_32 0.0 0 A 0.00000000 0.00000000 -molecule_0_33 0.0 0 A 0.00000000 0.00000000 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-molecule_0_78 0.0 0 A 0.00000000 0.00000000 -molecule_0_79 0.0 0 A 0.00000000 0.00000000 -molecule_0_80 0.0 0 A 0.00000000 0.00000000 -molecule_0_81 0.0 0 A 0.00000000 0.00000000 -molecule_0_82 0.0 0 A 0.00000000 0.00000000 -molecule_0_83 0.0 0 A 0.00000000 0.00000000 -molecule_0_84 0.0 0 A 0.00000000 0.00000000 -molecule_0_85 0.0 0 A 0.00000000 0.00000000 -molecule_0_86 0.0 0 A 0.00000000 0.00000000 -molecule_0_87 0.0 0 A 0.00000000 0.00000000 -molecule_0_88 0.0 0 A 0.00000000 0.00000000 -molecule_0_89 0.0 0 A 0.00000000 0.00000000 -molecule_0_90 0.0 0 A 0.00000000 0.00000000 -molecule_0_91 0.0 0 A 0.00000000 0.00000000 -molecule_0_92 0.0 0 A 0.00000000 0.00000000 -molecule_0_93 0.0 0 A 0.00000000 0.00000000 -molecule_0_94 0.0 0 A 0.00000000 0.00000000 -molecule_0_95 0.0 0 A 0.00000000 0.00000000 -molecule_0_96 0.0 0 A 0.00000000 0.00000000 -molecule_0_97 0.0 0 A 0.00000000 0.00000000 -molecule_0_98 0.0 0 A 0.00000000 0.00000000 -molecule_0_99 0.0 0 A 0.00000000 0.00000000 -molecule_0_100 0.0 0 A 0.00000000 0.00000000 -molecule_0_101 0.0 0 A 0.00000000 0.00000000 -molecule_0_102 0.0 0 A 0.00000000 0.00000000 -molecule_0_103 0.0 0 A 0.00000000 0.00000000 -molecule_0_104 0.0 0 A 0.00000000 0.00000000 -molecule_0_105 0.0 0 A 0.00000000 0.00000000 -molecule_0_106 0.0 0 A 0.00000000 0.00000000 -molecule_0_107 0.0 0 A 0.00000000 0.00000000 -molecule_0_108 0.0 0 A 0.00000000 0.00000000 -molecule_0_109 0.0 0 A 0.00000000 0.00000000 -molecule_0_110 0.0 0 A 0.00000000 0.00000000 -molecule_0_111 0.0 0 A 0.00000000 0.00000000 -molecule_0_112 0.0 0 A 0.00000000 0.00000000 -molecule_0_113 0.0 0 A 0.00000000 0.00000000 -molecule_0_114 0.0 0 A 0.00000000 0.00000000 -molecule_0_115 0.0 0 A 0.00000000 0.00000000 -molecule_0_116 0.0 0 A 0.00000000 0.00000000 -molecule_0_117 0.0 0 A 0.00000000 0.00000000 -molecule_0_118 0.0 0 A 0.00000000 0.00000000 -molecule_0_119 0.0 0 A 0.00000000 0.00000000 -molecule_0_120 0.0 0 A 0.00000000 0.00000000 -molecule_0_121 0.0 0 A 0.00000000 0.00000000 -molecule_0_122 0.0 0 A 0.00000000 0.00000000 -molecule_0_123 0.0 0 A 0.00000000 0.00000000 -molecule_0_124 0.0 0 A 0.00000000 0.00000000 -molecule_0_125 0.0 0 A 0.00000000 0.00000000 -molecule_0_126 0.0 0 A 0.00000000 0.00000000 -molecule_0_127 0.0 0 A 0.00000000 0.00000000 -molecule_0_128 0.0 0 A 0.00000000 0.00000000 -molecule_0_129 0.0 0 A 0.00000000 0.00000000 +molecule_1 0.0 0 A 0.00000000 0.00000000 +molecule_2 0.0 0 A 0.00000000 0.00000000 +molecule_3 0.0 0 A 0.00000000 0.00000000 +molecule_4 0.0 0 A 0.00000000 0.00000000 +molecule_5 0.0 0 A 0.00000000 0.00000000 +molecule_6 0.0 0 A 0.00000000 0.00000000 +molecule_7 0.0 0 A 0.00000000 0.00000000 +molecule_8 0.0 0 A 0.00000000 0.00000000 +molecule_9 0.0 0 A 0.00000000 0.00000000 +molecule_10 0.0 0 A 0.00000000 0.00000000 +molecule_11 0.0 0 A 0.00000000 0.00000000 +molecule_12 0.0 0 A 0.00000000 0.00000000 +molecule_13 0.0 0 A 0.00000000 0.00000000 +molecule_14 0.0 0 A 0.00000000 0.00000000 +molecule_15 0.0 0 A 0.00000000 0.00000000 +molecule_16 0.0 0 A 0.00000000 0.00000000 +molecule_17 0.0 0 A 0.00000000 0.00000000 +molecule_18 0.0 0 A 0.00000000 0.00000000 +molecule_19 0.0 0 A 0.00000000 0.00000000 +molecule_20 0.0 0 A 0.00000000 0.00000000 +molecule_21 0.0 0 A 0.00000000 0.00000000 +molecule_22 0.0 0 A 0.00000000 0.00000000 +molecule_23 0.0 0 A 0.00000000 0.00000000 +molecule_24 0.0 0 A 0.00000000 0.00000000 +molecule_25 0.0 0 A 0.00000000 0.00000000 +molecule_26 0.0 0 A 0.00000000 0.00000000 +molecule_27 0.0 0 A 0.00000000 0.00000000 +molecule_28 0.0 0 A 0.00000000 0.00000000 +molecule_29 0.0 0 A 0.00000000 0.00000000 +molecule_30 0.0 0 A 0.00000000 0.00000000 +molecule_31 0.0 0 A 0.00000000 0.00000000 +molecule_32 0.0 0 A 0.00000000 0.00000000 +molecule_33 0.0 0 A 0.00000000 0.00000000 +molecule_34 0.0 0 A 0.00000000 0.00000000 +molecule_35 0.0 0 A 0.00000000 0.00000000 +molecule_36 0.0 0 A 0.00000000 0.00000000 +molecule_37 0.0 0 A 0.00000000 0.00000000 +molecule_38 0.0 0 A 0.00000000 0.00000000 +molecule_39 0.0 0 A 0.00000000 0.00000000 +molecule_40 0.0 0 A 0.00000000 0.00000000 +molecule_41 0.0 0 A 0.00000000 0.00000000 +molecule_42 0.0 0 A 0.00000000 0.00000000 +molecule_43 0.0 0 A 0.00000000 0.00000000 +molecule_44 0.0 0 A 0.00000000 0.00000000 +molecule_45 0.0 0 A 0.00000000 0.00000000 +molecule_46 0.0 0 A 0.00000000 0.00000000 +molecule_47 0.0 0 A 0.00000000 0.00000000 +molecule_48 0.0 0 A 0.00000000 0.00000000 +molecule_49 0.0 0 A 0.00000000 0.00000000 +molecule_50 0.0 0 A 0.00000000 0.00000000 +molecule_51 0.0 0 A 0.00000000 0.00000000 +molecule_52 0.0 0 A 0.00000000 0.00000000 +molecule_53 0.0 0 A 0.00000000 0.00000000 +molecule_54 0.0 0 A 0.00000000 0.00000000 +molecule_55 0.0 0 A 0.00000000 0.00000000 +molecule_56 0.0 0 A 0.00000000 0.00000000 +molecule_57 0.0 0 A 0.00000000 0.00000000 +molecule_58 0.0 0 A 0.00000000 0.00000000 +molecule_59 0.0 0 A 0.00000000 0.00000000 +molecule_60 0.0 0 A 0.00000000 0.00000000 +molecule_61 0.0 0 A 0.00000000 0.00000000 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+molecule_85 0.0 0 A 0.00000000 0.00000000 +molecule_86 0.0 0 A 0.00000000 0.00000000 +molecule_87 0.0 0 A 0.00000000 0.00000000 +molecule_88 0.0 0 A 0.00000000 0.00000000 +molecule_89 0.0 0 A 0.00000000 0.00000000 +molecule_90 0.0 0 A 0.00000000 0.00000000 +molecule_91 0.0 0 A 0.00000000 0.00000000 +molecule_92 0.0 0 A 0.00000000 0.00000000 +molecule_93 0.0 0 A 0.00000000 0.00000000 +molecule_94 0.0 0 A 0.00000000 0.00000000 +molecule_95 0.0 0 A 0.00000000 0.00000000 +molecule_96 0.0 0 A 0.00000000 0.00000000 +molecule_97 0.0 0 A 0.00000000 0.00000000 +molecule_98 0.0 0 A 0.00000000 0.00000000 +molecule_99 0.0 0 A 0.00000000 0.00000000 +molecule_100 0.0 0 A 0.00000000 0.00000000 +molecule_101 0.0 0 A 0.00000000 0.00000000 +molecule_102 0.0 0 A 0.00000000 0.00000000 +molecule_103 0.0 0 A 0.00000000 0.00000000 +molecule_104 0.0 0 A 0.00000000 0.00000000 +molecule_105 0.0 0 A 0.00000000 0.00000000 +molecule_106 0.0 0 A 0.00000000 0.00000000 +molecule_107 0.0 0 A 0.00000000 0.00000000 +molecule_108 0.0 0 A 0.00000000 0.00000000 +molecule_109 0.0 0 A 0.00000000 0.00000000 +molecule_110 0.0 0 A 0.00000000 0.00000000 +molecule_111 0.0 0 A 0.00000000 0.00000000 +molecule_112 0.0 0 A 0.00000000 0.00000000 +molecule_113 0.0 0 A 0.00000000 0.00000000 +molecule_114 0.0 0 A 0.00000000 0.00000000 +molecule_115 0.0 0 A 0.00000000 0.00000000 +molecule_116 0.0 0 A 0.00000000 0.00000000 +molecule_117 0.0 0 A 0.00000000 0.00000000 +molecule_118 0.0 0 A 0.00000000 0.00000000 +molecule_119 0.0 0 A 0.00000000 0.00000000 +molecule_120 0.0 0 A 0.00000000 0.00000000 +molecule_121 0.0 0 A 0.00000000 0.00000000 +molecule_122 0.0 0 A 0.00000000 0.00000000 +molecule_123 0.0 0 A 0.00000000 0.00000000 +molecule_124 0.0 0 A 0.00000000 0.00000000 +molecule_125 0.0 0 A 0.00000000 0.00000000 +molecule_126 0.0 0 A 0.00000000 0.00000000 +molecule_127 0.0 0 A 0.00000000 0.00000000 +molecule_128 0.0 0 A 0.00000000 0.00000000 +molecule_129 0.0 0 A 0.00000000 0.00000000 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp index 1d80a41dd..1fb4a6712 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp @@ -1,305 +1,293 @@ [ nonbond_params ] -molecule_0_7 molecule_0_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 -molecule_0_8 molecule_0_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 -molecule_0_8 molecule_0_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 -molecule_0_9 molecule_0_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 -molecule_0_10 molecule_0_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 -molecule_0_11 molecule_0_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 -molecule_0_12 molecule_0_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 -molecule_0_13 molecule_0_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 -molecule_0_14 molecule_0_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 -molecule_0_15 molecule_0_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 -molecule_0_16 molecule_0_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 -molecule_0_17 molecule_0_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 -molecule_0_18 molecule_0_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 -molecule_0_20 molecule_0_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 -molecule_0_23 molecule_0_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 -molecule_0_24 molecule_0_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 -molecule_0_24 molecule_0_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 -molecule_0_25 molecule_0_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 -molecule_0_25 molecule_0_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 -molecule_0_25 molecule_0_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 -molecule_0_25 molecule_0_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 -molecule_0_27 molecule_0_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 -molecule_0_27 molecule_0_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 -molecule_0_28 molecule_0_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 -molecule_0_28 molecule_0_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 -molecule_0_28 molecule_0_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 -molecule_0_28 molecule_0_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 -molecule_0_29 molecule_0_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 -molecule_0_29 molecule_0_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 -molecule_0_29 molecule_0_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 -molecule_0_29 molecule_0_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 -molecule_0_30 molecule_0_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 -molecule_0_31 molecule_0_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 -molecule_0_32 molecule_0_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 -molecule_0_32 molecule_0_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 -molecule_0_33 molecule_0_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 -molecule_0_34 molecule_0_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 -molecule_0_35 molecule_0_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 -molecule_0_36 molecule_0_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 -molecule_0_37 molecule_0_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 -molecule_0_37 molecule_0_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 -molecule_0_38 molecule_0_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 -molecule_0_38 molecule_0_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 -molecule_0_38 molecule_0_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 -molecule_0_38 molecule_0_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 -molecule_0_38 molecule_0_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 -molecule_0_38 molecule_0_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 -molecule_0_38 molecule_0_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 -molecule_0_38 molecule_0_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 -molecule_0_39 molecule_0_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 -molecule_0_39 molecule_0_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 -molecule_0_40 molecule_0_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 -molecule_0_40 molecule_0_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 -molecule_0_41 molecule_0_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 -molecule_0_42 molecule_0_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 -molecule_0_44 molecule_0_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 -molecule_0_49 molecule_0_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 -molecule_0_50 molecule_0_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 -molecule_0_50 molecule_0_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 -molecule_0_51 molecule_0_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 -molecule_0_51 molecule_0_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 -molecule_0_51 molecule_0_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 -molecule_0_51 molecule_0_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 -molecule_0_52 molecule_0_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 -molecule_0_52 molecule_0_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 -molecule_0_52 molecule_0_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 -molecule_0_53 molecule_0_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 -molecule_0_53 molecule_0_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 -molecule_0_54 molecule_0_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 -molecule_0_54 molecule_0_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 -molecule_0_54 molecule_0_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 -molecule_0_55 molecule_0_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 -molecule_0_55 molecule_0_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 -molecule_0_55 molecule_0_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 -molecule_0_55 molecule_0_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 -molecule_0_55 molecule_0_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 -molecule_0_55 molecule_0_38 1 0.53863592 9.41400000 ;go bond 0.6045983765957093 -molecule_0_55 molecule_0_39 1 0.46884965 9.41400000 ;go bond 0.5262659343028784 -molecule_0_55 molecule_0_40 1 0.49397051 9.41400000 ;go bond 0.5544631488965023 -molecule_0_56 molecule_0_31 1 0.63305577 9.41400000 ;go bond 0.7105810801311345 -molecule_0_56 molecule_0_32 1 0.57070473 9.41400000 ;go bond 0.6405943964432239 -molecule_0_56 molecule_0_35 1 0.54499611 9.41400000 ;go bond 0.6117374504966917 -molecule_0_57 molecule_0_35 1 0.59142457 9.41400000 ;go bond 0.6638516326030536 -molecule_0_57 molecule_0_36 1 0.73443635 9.41400000 ;go bond 0.8243769340599911 -molecule_0_57 molecule_0_42 1 0.68123116 9.41400000 ;go bond 0.7646561231921536 -molecule_0_57 molecule_0_43 1 0.72932038 9.41400000 ;go bond 0.8186344517277264 -molecule_0_57 molecule_0_44 1 0.71017360 9.41400000 ;go bond 0.7971429108051539 -molecule_0_57 molecule_0_52 1 0.45255106 9.41400000 ;go bond 0.5079713907835711 -molecule_0_57 molecule_0_53 1 0.35572883 9.41400000 ;go bond 0.3992921109620664 -molecule_0_58 molecule_0_52 1 0.41486867 9.41400000 ;go bond 0.4656743363160884 -molecule_0_58 molecule_0_53 1 0.33528745 9.41400000 ;go bond 0.37634743770658646 -molecule_0_59 molecule_0_46 1 0.92985190 9.41400000 ;go bond 1.0437234628284975 -molecule_0_59 molecule_0_50 1 0.67865311 9.41400000 ;go bond 0.7617623567683692 -molecule_0_59 molecule_0_51 1 0.46599015 9.41400000 ;go bond 0.5230562584392384 -molecule_0_59 molecule_0_52 1 0.52411606 9.41400000 ;go bond 0.5883003833904864 -molecule_0_60 molecule_0_50 1 0.55757626 9.41400000 ;go bond 0.6258581889054639 -molecule_0_60 molecule_0_51 1 0.45353930 9.41400000 ;go bond 0.5090806492037284 -molecule_0_60 molecule_0_53 1 0.78554721 9.41400000 ;go bond 0.8817469319963909 -molecule_0_61 molecule_0_48 1 0.83253174 9.41400000 ;go bond 0.9344852838875899 -molecule_0_61 molecule_0_50 1 0.65515556 9.41400000 ;go bond 0.7353872567523113 -molecule_0_63 molecule_0_58 1 0.62967119 9.41400000 ;go bond 0.7067820082223201 -molecule_0_63 molecule_0_59 1 0.46427561 9.41400000 ;go bond 0.521131754230626 -molecule_0_64 molecule_0_53 1 0.82959737 9.41400000 ;go bond 0.9311915604701376 -molecule_0_64 molecule_0_60 1 0.38156281 9.41400000 ;go bond 0.4282897748904594 -molecule_0_66 molecule_0_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 -molecule_0_66 molecule_0_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 -molecule_0_68 molecule_0_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 -molecule_0_69 molecule_0_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 -molecule_0_69 molecule_0_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 -molecule_0_69 molecule_0_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 -molecule_0_69 molecule_0_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 -molecule_0_70 molecule_0_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 -molecule_0_72 molecule_0_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 -molecule_0_72 molecule_0_61 1 0.44682674 9.41400000 ;go bond 0.5015460538054222 -molecule_0_72 molecule_0_64 1 0.62949829 9.41400000 ;go bond 0.7065879353028186 -molecule_0_73 molecule_0_61 1 0.53130673 9.41400000 ;go bond 0.5963716385459682 -molecule_0_73 molecule_0_62 1 0.40729971 9.41400000 ;go bond 0.4571784705977002 -molecule_0_74 molecule_0_62 1 0.44897571 9.41400000 ;go bond 0.5039581950921611 -molecule_0_74 molecule_0_63 1 0.38506256 9.41400000 ;go bond 0.43221810950469636 -molecule_0_74 molecule_0_64 1 0.43052761 9.41400000 ;go bond 0.4832509069633833 -molecule_0_74 molecule_0_65 1 0.61184241 9.41400000 ;go bond 0.6867698876930867 -molecule_0_75 molecule_0_62 1 0.52199782 9.41400000 ;go bond 0.5859227452973559 -molecule_0_75 molecule_0_63 1 0.40610455 9.41400000 ;go bond 0.45583694740556885 -molecule_0_76 molecule_0_63 1 0.46409225 9.41400000 ;go bond 0.5209259369461889 -molecule_0_78 molecule_0_63 1 0.57576077 9.41400000 ;go bond 0.6462696105707938 -molecule_0_78 molecule_0_64 1 0.45724502 9.41400000 ;go bond 0.5132401787770625 -molecule_0_78 molecule_0_65 1 0.43974215 9.41400000 ;go bond 0.4935938729629976 -molecule_0_78 molecule_0_74 1 0.56052614 9.41400000 ;go bond 0.6291693208239874 -molecule_0_79 molecule_0_64 1 0.52803406 9.41400000 ;go bond 0.5926981930678074 -molecule_0_79 molecule_0_65 1 0.39916015 9.41400000 ;go bond 0.44804212253596193 -molecule_0_80 molecule_0_53 1 0.60673469 9.41400000 ;go bond 0.6810366626079589 -molecule_0_80 molecule_0_60 1 0.73868742 9.41400000 ;go bond 0.8291485950674535 -molecule_0_80 molecule_0_64 1 0.54789421 9.41400000 ;go bond 0.6149904606975389 -molecule_0_80 molecule_0_65 1 0.47057069 9.41400000 ;go bond 0.5281977457102484 -molecule_0_80 molecule_0_66 1 0.58883652 9.41400000 ;go bond 0.6609466408239479 -molecule_0_82 molecule_0_78 1 0.66632073 9.41400000 ;go bond 0.7479197331826131 -molecule_0_83 molecule_0_53 1 0.51788905 9.41400000 ;go bond 0.581310806103053 -molecule_0_83 molecule_0_54 1 0.51088855 9.41400000 ;go bond 0.5734530137551908 -molecule_0_83 molecule_0_58 1 0.70980394 9.41400000 ;go bond 0.7967279839859979 -molecule_0_83 molecule_0_64 1 0.89499397 9.41400000 ;go bond 1.0045967605887745 -molecule_0_83 molecule_0_78 1 0.81556181 9.41400000 ;go bond 0.9154371804917103 -molecule_0_84 molecule_0_40 1 0.40226578 9.41400000 ;go bond 0.45152806893595954 -molecule_0_84 molecule_0_41 1 0.48796771 9.41400000 ;go bond 0.5477252325235119 -molecule_0_84 molecule_0_42 1 0.63252675 9.41400000 ;go bond 0.7099872721863867 -molecule_0_84 molecule_0_43 1 0.89270990 9.41400000 ;go bond 1.0020329775751635 -molecule_0_84 molecule_0_53 1 0.66502200 9.41400000 ;go bond 0.7464619538686407 -molecule_0_84 molecule_0_54 1 0.56665258 9.41400000 ;go bond 0.6360460147186728 -molecule_0_85 molecule_0_40 1 0.48170210 9.41400000 ;go bond 0.5406923273735796 -molecule_0_85 molecule_0_81 1 0.64785523 9.41400000 ;go bond 0.7271929039256984 -molecule_0_86 molecule_0_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 -molecule_0_86 molecule_0_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 -molecule_0_86 molecule_0_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 -molecule_0_88 molecule_0_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 -molecule_0_88 molecule_0_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 -molecule_0_88 molecule_0_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 -molecule_0_88 molecule_0_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 -molecule_0_88 molecule_0_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 -molecule_0_88 molecule_0_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 -molecule_0_89 molecule_0_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 -molecule_0_89 molecule_0_15 1 0.69215886 9.41400000 ;go bond 0.7769220558398894 -molecule_0_90 molecule_0_78 1 0.80563795 9.41400000 ;go bond 0.9042980239792853 -molecule_0_90 molecule_0_82 1 0.59740893 9.41400000 ;go bond 0.6705688513824994 -molecule_0_90 molecule_0_83 1 0.57714934 9.41400000 ;go bond 0.6478282257424317 -molecule_0_91 molecule_0_55 1 0.70847337 9.41400000 ;go bond 0.7952344695348353 -molecule_0_91 molecule_0_58 1 0.76773720 9.41400000 ;go bond 0.8617558647944001 -molecule_0_91 molecule_0_83 1 0.57795007 9.41400000 ;go bond 0.6487270215620753 -molecule_0_92 molecule_0_15 1 0.66057405 9.41400000 ;go bond 0.741469302181026 -molecule_0_92 molecule_0_17 1 0.76276340 9.41400000 ;go bond 0.8561729710147924 -molecule_0_92 molecule_0_88 1 0.55891711 9.41400000 ;go bond 0.6273632448163519 -molecule_0_93 molecule_0_89 1 0.55091233 9.41400000 ;go bond 0.6183781864423775 -molecule_0_94 molecule_0_58 1 0.80192436 9.41400000 ;go bond 0.9001296640477775 -molecule_0_94 molecule_0_63 1 0.69400655 9.41400000 ;go bond 0.7789960144450432 -molecule_0_94 molecule_0_76 1 0.58706169 9.41400000 ;go bond 0.6589544684537765 -molecule_0_94 molecule_0_78 1 0.87593032 9.41400000 ;go bond 0.9831985419578763 -molecule_0_94 molecule_0_83 1 0.89829847 9.41400000 ;go bond 1.0083059444227724 -molecule_0_94 molecule_0_90 1 0.53696870 9.41400000 ;go bond 0.6027269866522963 -molecule_0_95 molecule_0_28 1 0.94028879 9.41400000 ;go bond 1.0554384813372668 -molecule_0_95 molecule_0_56 1 0.76727508 9.41400000 ;go bond 0.8612371596953154 -molecule_0_95 molecule_0_58 1 0.83998475 9.41400000 ;go bond 0.9428510053550558 -molecule_0_95 molecule_0_91 1 0.53148309 9.41400000 ;go bond 0.5965695928114466 -molecule_0_96 molecule_0_15 1 0.94537258 9.41400000 ;go bond 1.0611448446580265 -molecule_0_96 molecule_0_16 1 0.84805127 9.41400000 ;go bond 0.9519053644995195 -molecule_0_96 molecule_0_17 1 0.81454872 9.41400000 ;go bond 0.9143000281459933 -molecule_0_96 molecule_0_20 1 0.73587759 9.41400000 ;go bond 0.8259946673768416 -molecule_0_96 molecule_0_92 1 0.54860993 9.41400000 ;go bond 0.6157938252917854 -molecule_0_97 molecule_0_63 1 0.84557275 9.41400000 ;go bond 0.9491233248865086 -molecule_0_97 molecule_0_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 -molecule_0_97 molecule_0_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 -molecule_0_98 molecule_0_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 -molecule_0_98 molecule_0_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 -molecule_0_98 molecule_0_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 -molecule_0_99 molecule_0_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 -molecule_0_99 molecule_0_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 -molecule_0_99 molecule_0_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 -molecule_0_99 molecule_0_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 -molecule_0_100 molecule_0_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 -molecule_0_100 molecule_0_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 -molecule_0_100 molecule_0_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 -molecule_0_101 molecule_0_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 -molecule_0_104 molecule_0_23 1 0.90496194 9.41400000 ;go bond 1.0157854279713863 -molecule_0_104 molecule_0_99 1 0.37779975 9.41400000 ;go bond 0.42406587714866395 -molecule_0_105 molecule_0_23 1 0.85792539 9.41400000 ;go bond 0.9629886926477136 -molecule_0_105 molecule_0_27 1 0.80028132 9.41400000 ;go bond 0.8982854095190085 -molecule_0_105 molecule_0_28 1 0.85914649 9.41400000 ;go bond 0.9643593287596212 -molecule_0_105 molecule_0_31 1 0.84674626 9.41400000 ;go bond 0.950440544780807 -molecule_0_105 molecule_0_99 1 0.58741430 9.41400000 ;go bond 0.6593502594081683 -molecule_0_107 molecule_0_98 1 0.70183885 9.41400000 ;go bond 0.7877874714268905 -molecule_0_108 molecule_0_28 1 0.92956079 9.41400000 ;go bond 1.0433967044744268 -molecule_0_108 molecule_0_35 1 0.82960839 9.41400000 ;go bond 0.9312039368635526 -molecule_0_108 molecule_0_56 1 0.78133210 9.41400000 ;go bond 0.8770156294387439 -molecule_0_108 molecule_0_57 1 0.77168204 9.41400000 ;go bond 0.8661838041857776 -molecule_0_108 molecule_0_98 1 0.90403083 9.41400000 ;go bond 1.014740292066367 -molecule_0_108 molecule_0_99 1 0.90315750 9.41400000 ;go bond 1.0137600206889819 -molecule_0_110 molecule_0_34 1 0.54869664 9.41400000 ;go bond 0.6158911542488904 -molecule_0_110 molecule_0_35 1 0.64980269 9.41400000 ;go bond 0.7293788607697123 -molecule_0_111 molecule_0_27 1 0.70311941 9.41400000 ;go bond 0.7892248529963473 -molecule_0_111 molecule_0_31 1 0.56259884 9.41400000 ;go bond 0.6314958500157425 -molecule_0_111 molecule_0_105 1 0.59346888 9.41400000 ;go bond 0.6661462995266982 -molecule_0_111 molecule_0_106 1 0.59882239 9.41400000 ;go bond 0.6721554100763635 -molecule_0_112 molecule_0_106 1 0.57753815 9.41400000 ;go bond 0.6482646568405853 -molecule_0_112 molecule_0_107 1 0.74260248 9.41400000 ;go bond 0.833543103918769 -molecule_0_112 molecule_0_108 1 0.53753958 9.41400000 ;go bond 0.603367775987529 -molecule_0_113 molecule_0_109 1 0.53306219 9.41400000 ;go bond 0.5983420831461288 -molecule_0_114 molecule_0_34 1 0.72771145 9.41400000 ;go bond 0.8168284821715603 -molecule_0_114 molecule_0_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 -molecule_0_115 molecule_0_30 1 0.62277169 9.41400000 ;go bond 0.6990375917289473 -molecule_0_115 molecule_0_31 1 0.71820218 9.41400000 ;go bond 0.8061546928175227 -molecule_0_115 molecule_0_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 -molecule_0_115 molecule_0_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 -molecule_0_115 molecule_0_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 -molecule_0_116 molecule_0_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 -molecule_0_116 molecule_0_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 -molecule_0_116 molecule_0_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 -molecule_0_118 molecule_0_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 -molecule_0_120 molecule_0_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 -molecule_0_120 molecule_0_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 -molecule_0_120 molecule_0_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 -molecule_0_120 molecule_0_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 -molecule_0_120 molecule_0_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 -molecule_0_122 molecule_0_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 -molecule_0_123 molecule_0_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 -molecule_0_123 molecule_0_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 -molecule_0_123 molecule_0_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 -molecule_0_123 molecule_0_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 -molecule_0_123 molecule_0_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 -molecule_0_123 molecule_0_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 -molecule_0_124 molecule_0_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 -molecule_0_124 molecule_0_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 -molecule_0_124 molecule_0_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 -molecule_0_124 molecule_0_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 -molecule_0_124 molecule_0_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 -molecule_0_125 molecule_0_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 -molecule_0_125 molecule_0_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 -molecule_0_127 molecule_0_5 1 0.79805432 9.41400000 ;go bond 0.8957856911439042 -molecule_0_127 molecule_0_6 1 0.59870073 9.41400000 ;go bond 0.6720188457372778 -molecule_0_129 molecule_0_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 -molecule_0_129 molecule_0_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 -molecule_0_129 molecule_0_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 -molecule_0_129 molecule_0_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 -W molecule_0_1 1 0.47000000 1.00000000 ;water bias C -W molecule_0_2 1 0.41000000 -0.50000000 ;water bias E -W molecule_0_3 1 0.47000000 1.00000000 ;water bias C -W molecule_0_4 1 0.41000000 1.00000000 ;water bias C -W molecule_0_9 1 0.41000000 -1.00000000 ;water bias H -W molecule_0_10 1 0.41000000 -1.00000000 ;water bias H -W molecule_0_17 1 0.47000000 1.00000000 ;water bias C -W molecule_0_20 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_23 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_24 1 0.47000000 1.00000000 ;water bias C -W molecule_0_29 1 0.41000000 -1.00000000 ;water bias H -W molecule_0_30 1 0.47000000 -1.00000000 ;water bias H -W molecule_0_31 1 0.41000000 -1.00000000 ;water bias H -W molecule_0_32 1 0.41000000 -1.00000000 ;water bias H -W molecule_0_39 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_42 1 0.41000000 1.00000000 ;water bias C -W molecule_0_43 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_44 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_45 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_46 1 0.47000000 1.00000000 ;water bias C -W molecule_0_50 1 0.47000000 1.00000000 ;water bias C -W molecule_0_51 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_52 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_53 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_58 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_59 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_64 1 0.47000000 1.00000000 ;water bias C -W molecule_0_65 1 0.47000000 -0.50000000 ;water bias E -W molecule_0_66 1 0.47000000 1.00000000 ;water bias C -W molecule_0_68 1 0.47000000 1.00000000 ;water bias C -W molecule_0_69 1 0.47000000 1.00000000 ;water bias C -W molecule_0_72 1 0.47000000 1.00000000 ;water bias C -W molecule_0_73 1 0.47000000 1.00000000 ;water bias C -W molecule_0_74 1 0.47000000 1.00000000 ;water bias C -W molecule_0_77 1 0.47000000 1.00000000 ;water bias C -W molecule_0_79 1 0.41000000 -0.50000000 ;water bias E -W molecule_0_88 1 0.47000000 1.00000000 ;water bias C -W molecule_0_93 1 0.47000000 -1.00000000 ;water bias H -W molecule_0_94 1 0.47000000 -1.00000000 ;water bias H -W molecule_0_95 1 0.41000000 -1.00000000 ;water bias H -W molecule_0_96 1 0.47000000 -1.00000000 ;water bias H -W molecule_0_119 1 0.47000000 1.00000000 ;water bias C -W molecule_0_127 1 0.47000000 1.00000000 ;water bias C -W molecule_0_128 1 0.47000000 1.00000000 ;water bias C -W molecule_0_129 1 0.47000000 1.00000000 ;water bias C +molecule_7 molecule_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 +molecule_8 molecule_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 +molecule_8 molecule_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 +molecule_9 molecule_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 +molecule_10 molecule_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 +molecule_11 molecule_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 +molecule_12 molecule_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 +molecule_13 molecule_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 +molecule_14 molecule_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 +molecule_15 molecule_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 +molecule_16 molecule_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 +molecule_17 molecule_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 +molecule_18 molecule_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 +molecule_20 molecule_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 +molecule_23 molecule_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 +molecule_24 molecule_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 +molecule_24 molecule_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 +molecule_25 molecule_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 +molecule_25 molecule_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 +molecule_25 molecule_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 +molecule_25 molecule_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 +molecule_27 molecule_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 +molecule_27 molecule_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 +molecule_28 molecule_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 +molecule_28 molecule_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 +molecule_28 molecule_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 +molecule_28 molecule_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 +molecule_29 molecule_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 +molecule_29 molecule_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 +molecule_29 molecule_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 +molecule_29 molecule_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 +molecule_30 molecule_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 +molecule_31 molecule_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 +molecule_32 molecule_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 +molecule_32 molecule_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 +molecule_33 molecule_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 +molecule_34 molecule_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 +molecule_35 molecule_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 +molecule_36 molecule_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 +molecule_37 molecule_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 +molecule_37 molecule_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 +molecule_38 molecule_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 +molecule_38 molecule_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 +molecule_38 molecule_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 +molecule_38 molecule_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 +molecule_38 molecule_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 +molecule_38 molecule_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 +molecule_38 molecule_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 +molecule_38 molecule_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 +molecule_39 molecule_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 +molecule_39 molecule_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 +molecule_40 molecule_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 +molecule_40 molecule_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 +molecule_41 molecule_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 +molecule_42 molecule_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 +molecule_44 molecule_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 +molecule_49 molecule_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 +molecule_50 molecule_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 +molecule_50 molecule_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 +molecule_51 molecule_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 +molecule_51 molecule_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 +molecule_51 molecule_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 +molecule_51 molecule_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 +molecule_52 molecule_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 +molecule_52 molecule_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 +molecule_52 molecule_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 +molecule_53 molecule_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 +molecule_53 molecule_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 +molecule_54 molecule_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 +molecule_54 molecule_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 +molecule_54 molecule_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 +molecule_55 molecule_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 +molecule_55 molecule_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 +molecule_55 molecule_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 +molecule_55 molecule_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 +molecule_55 molecule_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 +molecule_55 molecule_38 1 0.53863592 9.41400000 ;go bond 0.6045983765957093 +molecule_55 molecule_39 1 0.46884965 9.41400000 ;go bond 0.5262659343028784 +molecule_55 molecule_40 1 0.49397051 9.41400000 ;go bond 0.5544631488965023 +molecule_56 molecule_31 1 0.63305577 9.41400000 ;go bond 0.7105810801311345 +molecule_56 molecule_32 1 0.57070473 9.41400000 ;go bond 0.6405943964432239 +molecule_56 molecule_35 1 0.54499611 9.41400000 ;go bond 0.6117374504966917 +molecule_57 molecule_35 1 0.59142457 9.41400000 ;go bond 0.6638516326030536 +molecule_57 molecule_36 1 0.73443635 9.41400000 ;go bond 0.8243769340599911 +molecule_57 molecule_42 1 0.68123116 9.41400000 ;go bond 0.7646561231921536 +molecule_57 molecule_43 1 0.72932038 9.41400000 ;go bond 0.8186344517277264 +molecule_57 molecule_44 1 0.71017360 9.41400000 ;go bond 0.7971429108051539 +molecule_57 molecule_52 1 0.45255106 9.41400000 ;go bond 0.5079713907835711 +molecule_57 molecule_53 1 0.35572883 9.41400000 ;go bond 0.3992921109620664 +molecule_58 molecule_52 1 0.41486867 9.41400000 ;go bond 0.4656743363160884 +molecule_58 molecule_53 1 0.33528745 9.41400000 ;go bond 0.37634743770658646 +molecule_59 molecule_46 1 0.92985190 9.41400000 ;go bond 1.0437234628284975 +molecule_59 molecule_50 1 0.67865311 9.41400000 ;go bond 0.7617623567683692 +molecule_59 molecule_51 1 0.46599015 9.41400000 ;go bond 0.5230562584392384 +molecule_59 molecule_52 1 0.52411606 9.41400000 ;go bond 0.5883003833904864 +molecule_60 molecule_50 1 0.55757626 9.41400000 ;go bond 0.6258581889054639 +molecule_60 molecule_51 1 0.45353930 9.41400000 ;go bond 0.5090806492037284 +molecule_60 molecule_53 1 0.78554721 9.41400000 ;go bond 0.8817469319963909 +molecule_61 molecule_48 1 0.83253174 9.41400000 ;go bond 0.9344852838875899 +molecule_61 molecule_50 1 0.65515556 9.41400000 ;go bond 0.7353872567523113 +molecule_63 molecule_58 1 0.62967119 9.41400000 ;go bond 0.7067820082223201 +molecule_63 molecule_59 1 0.46427561 9.41400000 ;go bond 0.521131754230626 +molecule_64 molecule_53 1 0.82959737 9.41400000 ;go bond 0.9311915604701376 +molecule_64 molecule_60 1 0.38156281 9.41400000 ;go bond 0.4282897748904594 +molecule_66 molecule_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 +molecule_66 molecule_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 +molecule_68 molecule_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 +molecule_69 molecule_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 +molecule_69 molecule_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 +molecule_69 molecule_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 +molecule_69 molecule_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 +molecule_70 molecule_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 +molecule_72 molecule_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 +molecule_72 molecule_61 1 0.44682674 9.41400000 ;go bond 0.5015460538054222 +molecule_72 molecule_64 1 0.62949829 9.41400000 ;go bond 0.7065879353028186 +molecule_73 molecule_61 1 0.53130673 9.41400000 ;go bond 0.5963716385459682 +molecule_73 molecule_62 1 0.40729971 9.41400000 ;go bond 0.4571784705977002 +molecule_74 molecule_62 1 0.44897571 9.41400000 ;go bond 0.5039581950921611 +molecule_74 molecule_63 1 0.38506256 9.41400000 ;go bond 0.43221810950469636 +molecule_74 molecule_64 1 0.43052761 9.41400000 ;go bond 0.4832509069633833 +molecule_74 molecule_65 1 0.61184241 9.41400000 ;go bond 0.6867698876930867 +molecule_75 molecule_62 1 0.52199782 9.41400000 ;go bond 0.5859227452973559 +molecule_75 molecule_63 1 0.40610455 9.41400000 ;go bond 0.45583694740556885 +molecule_76 molecule_63 1 0.46409225 9.41400000 ;go bond 0.5209259369461889 +molecule_78 molecule_63 1 0.57576077 9.41400000 ;go bond 0.6462696105707938 +molecule_78 molecule_65 1 0.43974215 9.41400000 ;go bond 0.4935938729629976 +molecule_78 molecule_74 1 0.56052614 9.41400000 ;go bond 0.6291693208239874 +molecule_80 molecule_53 1 0.60673469 9.41400000 ;go bond 0.6810366626079589 +molecule_80 molecule_60 1 0.73868742 9.41400000 ;go bond 0.8291485950674535 +molecule_82 molecule_78 1 0.66632073 9.41400000 ;go bond 0.7479197331826131 +molecule_83 molecule_53 1 0.51788905 9.41400000 ;go bond 0.581310806103053 +molecule_83 molecule_54 1 0.51088855 9.41400000 ;go bond 0.5734530137551908 +molecule_83 molecule_58 1 0.70980394 9.41400000 ;go bond 0.7967279839859979 +molecule_83 molecule_64 1 0.89499397 9.41400000 ;go bond 1.0045967605887745 +molecule_83 molecule_78 1 0.81556181 9.41400000 ;go bond 0.9154371804917103 +molecule_84 molecule_40 1 0.40226578 9.41400000 ;go bond 0.45152806893595954 +molecule_84 molecule_41 1 0.48796771 9.41400000 ;go bond 0.5477252325235119 +molecule_84 molecule_42 1 0.63252675 9.41400000 ;go bond 0.7099872721863867 +molecule_84 molecule_43 1 0.89270990 9.41400000 ;go bond 1.0020329775751635 +molecule_84 molecule_53 1 0.66502200 9.41400000 ;go bond 0.7464619538686407 +molecule_84 molecule_54 1 0.56665258 9.41400000 ;go bond 0.6360460147186728 +molecule_85 molecule_40 1 0.48170210 9.41400000 ;go bond 0.5406923273735796 +molecule_85 molecule_81 1 0.64785523 9.41400000 ;go bond 0.7271929039256984 +molecule_86 molecule_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 +molecule_86 molecule_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 +molecule_86 molecule_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 +molecule_88 molecule_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 +molecule_88 molecule_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 +molecule_88 molecule_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 +molecule_88 molecule_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 +molecule_88 molecule_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 +molecule_88 molecule_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 +molecule_89 molecule_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 +molecule_89 molecule_15 1 0.69215886 9.41400000 ;go bond 0.7769220558398894 +molecule_90 molecule_78 1 0.80563795 9.41400000 ;go bond 0.9042980239792853 +molecule_90 molecule_82 1 0.59740893 9.41400000 ;go bond 0.6705688513824994 +molecule_90 molecule_83 1 0.57714934 9.41400000 ;go bond 0.6478282257424317 +molecule_91 molecule_55 1 0.70847337 9.41400000 ;go bond 0.7952344695348353 +molecule_91 molecule_58 1 0.76773720 9.41400000 ;go bond 0.8617558647944001 +molecule_91 molecule_83 1 0.57795007 9.41400000 ;go bond 0.6487270215620753 +molecule_92 molecule_15 1 0.66057405 9.41400000 ;go bond 0.741469302181026 +molecule_92 molecule_17 1 0.76276340 9.41400000 ;go bond 0.8561729710147924 +molecule_92 molecule_88 1 0.55891711 9.41400000 ;go bond 0.6273632448163519 +molecule_93 molecule_89 1 0.55091233 9.41400000 ;go bond 0.6183781864423775 +molecule_94 molecule_58 1 0.80192436 9.41400000 ;go bond 0.9001296640477775 +molecule_94 molecule_63 1 0.69400655 9.41400000 ;go bond 0.7789960144450432 +molecule_94 molecule_83 1 0.89829847 9.41400000 ;go bond 1.0083059444227724 +molecule_94 molecule_90 1 0.53696870 9.41400000 ;go bond 0.6027269866522963 +molecule_95 molecule_28 1 0.94028879 9.41400000 ;go bond 1.0554384813372668 +molecule_95 molecule_56 1 0.76727508 9.41400000 ;go bond 0.8612371596953154 +molecule_95 molecule_58 1 0.83998475 9.41400000 ;go bond 0.9428510053550558 +molecule_95 molecule_91 1 0.53148309 9.41400000 ;go bond 0.5965695928114466 +molecule_96 molecule_15 1 0.94537258 9.41400000 ;go bond 1.0611448446580265 +molecule_96 molecule_16 1 0.84805127 9.41400000 ;go bond 0.9519053644995195 +molecule_96 molecule_17 1 0.81454872 9.41400000 ;go bond 0.9143000281459933 +molecule_96 molecule_20 1 0.73587759 9.41400000 ;go bond 0.8259946673768416 +molecule_96 molecule_92 1 0.54860993 9.41400000 ;go bond 0.6157938252917854 +molecule_97 molecule_63 1 0.84557275 9.41400000 ;go bond 0.9491233248865086 +molecule_97 molecule_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 +molecule_97 molecule_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 +molecule_98 molecule_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 +molecule_98 molecule_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 +molecule_98 molecule_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 +molecule_99 molecule_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 +molecule_99 molecule_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 +molecule_99 molecule_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 +molecule_99 molecule_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 +molecule_100 molecule_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 +molecule_100 molecule_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 +molecule_100 molecule_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 +molecule_101 molecule_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 +molecule_104 molecule_23 1 0.90496194 9.41400000 ;go bond 1.0157854279713863 +molecule_104 molecule_99 1 0.37779975 9.41400000 ;go bond 0.42406587714866395 +molecule_105 molecule_23 1 0.85792539 9.41400000 ;go bond 0.9629886926477136 +molecule_105 molecule_27 1 0.80028132 9.41400000 ;go bond 0.8982854095190085 +molecule_105 molecule_28 1 0.85914649 9.41400000 ;go bond 0.9643593287596212 +molecule_105 molecule_31 1 0.84674626 9.41400000 ;go bond 0.950440544780807 +molecule_105 molecule_99 1 0.58741430 9.41400000 ;go bond 0.6593502594081683 +molecule_107 molecule_98 1 0.70183885 9.41400000 ;go bond 0.7877874714268905 +molecule_108 molecule_28 1 0.92956079 9.41400000 ;go bond 1.0433967044744268 +molecule_108 molecule_35 1 0.82960839 9.41400000 ;go bond 0.9312039368635526 +molecule_108 molecule_56 1 0.78133210 9.41400000 ;go bond 0.8770156294387439 +molecule_108 molecule_57 1 0.77168204 9.41400000 ;go bond 0.8661838041857776 +molecule_108 molecule_98 1 0.90403083 9.41400000 ;go bond 1.014740292066367 +molecule_108 molecule_99 1 0.90315750 9.41400000 ;go bond 1.0137600206889819 +molecule_110 molecule_34 1 0.54869664 9.41400000 ;go bond 0.6158911542488904 +molecule_110 molecule_35 1 0.64980269 9.41400000 ;go bond 0.7293788607697123 +molecule_111 molecule_27 1 0.70311941 9.41400000 ;go bond 0.7892248529963473 +molecule_111 molecule_31 1 0.56259884 9.41400000 ;go bond 0.6314958500157425 +molecule_111 molecule_105 1 0.59346888 9.41400000 ;go bond 0.6661462995266982 +molecule_111 molecule_106 1 0.59882239 9.41400000 ;go bond 0.6721554100763635 +molecule_112 molecule_106 1 0.57753815 9.41400000 ;go bond 0.6482646568405853 +molecule_112 molecule_107 1 0.74260248 9.41400000 ;go bond 0.833543103918769 +molecule_112 molecule_108 1 0.53753958 9.41400000 ;go bond 0.603367775987529 +molecule_113 molecule_109 1 0.53306219 9.41400000 ;go bond 0.5983420831461288 +molecule_114 molecule_34 1 0.72771145 9.41400000 ;go bond 0.8168284821715603 +molecule_114 molecule_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 +molecule_115 molecule_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 +molecule_115 molecule_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 +molecule_115 molecule_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 +molecule_116 molecule_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 +molecule_116 molecule_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 +molecule_116 molecule_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 +molecule_118 molecule_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 +molecule_120 molecule_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 +molecule_120 molecule_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 +molecule_120 molecule_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 +molecule_120 molecule_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 +molecule_120 molecule_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 +molecule_122 molecule_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 +molecule_123 molecule_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 +molecule_123 molecule_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 +molecule_123 molecule_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 +molecule_123 molecule_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 +molecule_123 molecule_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 +molecule_123 molecule_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 +molecule_124 molecule_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 +molecule_124 molecule_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 +molecule_124 molecule_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 +molecule_124 molecule_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 +molecule_124 molecule_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 +molecule_125 molecule_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 +molecule_125 molecule_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 +molecule_129 molecule_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 +molecule_129 molecule_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 +molecule_129 molecule_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 +molecule_129 molecule_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 +W molecule_1 1 0.47000000 1.00000000 ;water bias C +W molecule_2 1 0.41000000 -0.50000000 ;water bias E +W molecule_3 1 0.47000000 1.00000000 ;water bias C +W molecule_4 1 0.41000000 1.00000000 ;water bias C +W molecule_9 1 0.41000000 -1.00000000 ;water bias H +W molecule_10 1 0.41000000 -1.00000000 ;water bias H +W molecule_17 1 0.47000000 1.00000000 ;water bias C +W molecule_20 1 0.47000000 -0.50000000 ;water bias E +W molecule_23 1 0.47000000 -0.50000000 ;water bias E +W molecule_24 1 0.47000000 1.00000000 ;water bias C +W molecule_29 1 0.41000000 -1.00000000 ;water bias H +W molecule_30 1 0.47000000 -1.00000000 ;water bias H +W molecule_31 1 0.41000000 -1.00000000 ;water bias H +W molecule_32 1 0.41000000 -1.00000000 ;water bias H +W molecule_39 1 0.47000000 -0.50000000 ;water bias E +W molecule_42 1 0.41000000 1.00000000 ;water bias C +W molecule_43 1 0.47000000 -0.50000000 ;water bias E +W molecule_44 1 0.47000000 -0.50000000 ;water bias E +W molecule_45 1 0.47000000 -0.50000000 ;water bias E +W molecule_46 1 0.47000000 1.00000000 ;water bias C +W molecule_50 1 0.47000000 1.00000000 ;water bias C +W molecule_51 1 0.47000000 -0.50000000 ;water bias E +W molecule_52 1 0.47000000 -0.50000000 ;water bias E +W molecule_53 1 0.47000000 -0.50000000 ;water bias E +W molecule_58 1 0.47000000 -0.50000000 ;water bias E +W molecule_59 1 0.47000000 -0.50000000 ;water bias E +W molecule_64 1 0.47000000 1.00000000 ;water bias C +W molecule_65 1 0.47000000 -0.50000000 ;water bias E +W molecule_66 1 0.47000000 1.00000000 ;water bias C +W molecule_68 1 0.47000000 1.00000000 ;water bias C +W molecule_69 1 0.47000000 1.00000000 ;water bias C +W molecule_72 1 0.47000000 1.00000000 ;water bias C +W molecule_73 1 0.47000000 1.00000000 ;water bias C +W molecule_74 1 0.47000000 1.00000000 ;water bias C +W molecule_77 1 0.47000000 1.00000000 ;water bias C +W molecule_79 1 0.41000000 -0.50000000 ;water bias E +W molecule_88 1 0.47000000 1.00000000 ;water bias C +W molecule_93 1 0.47000000 -1.00000000 ;water bias H +W molecule_94 1 0.47000000 -1.00000000 ;water bias H +W molecule_95 1 0.41000000 -1.00000000 ;water bias H +W molecule_96 1 0.47000000 -1.00000000 ;water bias H +W molecule_119 1 0.47000000 1.00000000 ;water bias C +W molecule_127 1 0.47000000 1.00000000 ;water bias C +W molecule_128 1 0.47000000 1.00000000 ;water bias C +W molecule_129 1 0.47000000 1.00000000 ;water bias C From 93a59ba80ce935931547c6903c88f770524de205 Mon Sep 17 00:00:00 2001 From: csbrasnett Date: Mon, 28 Oct 2024 13:16:20 +0100 Subject: [PATCH 4/6] fix test failures --- .../lysozyme_GO/martinize2/molecule_0.itp | 1669 ----------------- .../tier-1/lysozyme_GO/martinize2/topol.top | 4 +- .../lysozyme_GObias/martinize2/molecule_0.itp | 1669 ----------------- .../lysozyme_GObias/martinize2/topol.top | 4 +- 4 files changed, 4 insertions(+), 3342 deletions(-) delete mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp delete mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp deleted file mode 100644 index 501335e6f..000000000 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp +++ /dev/null @@ -1,1669 +0,0 @@ -; This file was generated using the following command: -; /local/lborge01/martinize_stuff/dev_go/devmartinize/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go -go-map ../map.map -; martinize with vermouth 0.9.7.dev79 -; The following sequence of secondary structure -; was used for the full system: -; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC - -; Pleas cite the following papers: -; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 - -[ moleculetype ] -molecule_0 1 - -[ atoms ] - 1 Q5 1 LYS BB 1 1 - 2 SC3 1 LYS SC1 2 0.0 - 3 SQ4p 1 LYS SC2 3 1.0 - 4 SP2 2 VAL BB 4 0.0 - 5 SC3 2 VAL SC1 5 0.0 - 6 P2 3 PHE BB 6 0.0 - 7 SC4 3 PHE SC1 7 0.0 - 8 TC5 3 PHE SC2 8 0.0 - 9 TC5 3 PHE SC3 9 0.0 - 10 SP1 4 GLY BB 10 0.0 - 11 P2 5 ARG BB 11 0.0 - 12 SC3 5 ARG SC1 12 0.0 - 13 SQ3p 5 ARG SC2 13 1.0 - 14 P2 6 CYS BB 14 0.0 - 15 TC6 6 CYS SC1 15 0.0 - 16 P2 7 GLU BB 16 0.0 - 17 Q5n 7 GLU SC1 17 -1.0 - 18 P2 8 LEU BB 18 0.0 - 19 SC2 8 LEU SC1 19 0.0 - 20 SP2 9 ALA BB 20 0.0 - 21 TC3 9 ALA SC1 21 0.0 - 22 SP2 10 ALA BB 22 0.0 - 23 TC3 10 ALA SC1 23 0.0 - 24 SP2 11 ALA BB 24 0.0 - 25 TC3 11 ALA SC1 25 0.0 - 26 P2 12 MET BB 26 0.0 - 27 C6 12 MET SC1 27 0.0 - 28 P2 13 LYS BB 28 0.0 - 29 SC3 13 LYS SC1 29 0.0 - 30 SQ4p 13 LYS SC2 30 1.0 - 31 P2 14 ARG BB 31 0.0 - 32 SC3 14 ARG SC1 32 0.0 - 33 SQ3p 14 ARG SC2 33 1.0 - 34 P2 15 HIS BB 34 0.0 - 35 TC4 15 HIS SC1 35 0.0 - 36 TN6d 15 HIS SC2 36 0.0 - 37 TN5a 15 HIS SC3 37 0.0 - 38 SP1 16 GLY BB 38 0.0 - 39 P2 17 LEU BB 39 0.0 - 40 SC2 17 LEU SC1 40 0.0 - 41 P2 18 ASP BB 41 0.0 - 42 SQ5n 18 ASP SC1 42 -1.0 - 43 P2 19 ASN BB 43 0.0 - 44 SP5 19 ASN SC1 44 0.0 - 45 P2 20 TYR BB 45 0.0 - 46 TC4 20 TYR SC1 46 0.0 - 47 TC5 20 TYR SC2 47 0.0 - 48 TC5 20 TYR SC3 48 0.0 - 49 TN6 20 TYR SC4 49 0.0 - 50 P2 21 ARG BB 50 0.0 - 51 SC3 21 ARG SC1 51 0.0 - 52 SQ3p 21 ARG SC2 52 1.0 - 53 SP1 22 GLY BB 53 0.0 - 54 P2 23 TYR BB 54 0.0 - 55 TC4 23 TYR SC1 55 0.0 - 56 TC5 23 TYR SC2 56 0.0 - 57 TC5 23 TYR SC3 57 0.0 - 58 TN6 23 TYR SC4 58 0.0 - 59 P2 24 SER BB 59 0.0 - 60 TP1 24 SER SC1 60 0.0 - 61 P2 25 LEU BB 61 0.0 - 62 SC2 25 LEU SC1 62 0.0 - 63 SP1 26 GLY BB 63 0.0 - 64 P2 27 ASN BB 64 0.0 - 65 SP5 27 ASN SC1 65 0.0 - 66 P2 28 TRP BB 66 0.0 - 67 TC4 28 TRP SC1 67 0.0 36.0 - 68 TN6d 28 TRP SC2 68 0.0 36.0 - 69 TC5 28 TRP SC3 69 0.0 0.0 - 70 TC5 28 TRP SC4 70 0.0 36.0 - 71 TC5 28 TRP SC5 71 0.0 36.0 - 72 SP2 29 VAL BB 72 0.0 - 73 SC3 29 VAL SC1 73 0.0 - 74 P2 30 CYS BB 74 0.0 - 75 TC6 30 CYS SC1 75 0.0 - 76 SP2 31 ALA BB 76 0.0 - 77 TC3 31 ALA SC1 77 0.0 - 78 SP2 32 ALA BB 78 0.0 - 79 TC3 32 ALA SC1 79 0.0 - 80 P2 33 LYS BB 80 0.0 - 81 SC3 33 LYS SC1 81 0.0 - 82 SQ4p 33 LYS SC2 82 1.0 - 83 P2 34 PHE BB 83 0.0 - 84 SC4 34 PHE SC1 84 0.0 - 85 TC5 34 PHE SC2 85 0.0 - 86 TC5 34 PHE SC3 86 0.0 - 87 P2 35 GLU BB 87 0.0 - 88 Q5n 35 GLU SC1 88 -1.0 - 89 P2 36 SER BB 89 0.0 - 90 TP1 36 SER SC1 90 0.0 - 91 P2 37 ASN BB 91 0.0 - 92 SP5 37 ASN SC1 92 0.0 - 93 P2 38 PHE BB 93 0.0 - 94 SC4 38 PHE SC1 94 0.0 - 95 TC5 38 PHE SC2 95 0.0 - 96 TC5 38 PHE SC3 96 0.0 - 97 P2 39 ASN BB 97 0.0 - 98 SP5 39 ASN SC1 98 0.0 - 99 P2 40 THR BB 99 0.0 -100 SP1 40 THR SC1 100 0.0 -101 P2 41 GLN BB 101 0.0 -102 P5 41 GLN SC1 102 0.0 -103 SP2 42 ALA BB 103 0.0 -104 TC3 42 ALA SC1 104 0.0 -105 P2 43 THR BB 105 0.0 -106 SP1 43 THR SC1 106 0.0 -107 P2 44 ASN BB 107 0.0 -108 SP5 44 ASN SC1 108 0.0 -109 P2 45 ARG BB 109 0.0 -110 SC3 45 ARG SC1 110 0.0 -111 SQ3p 45 ARG SC2 111 1.0 -112 P2 46 ASN BB 112 0.0 -113 SP5 46 ASN SC1 113 0.0 -114 P2 47 THR BB 114 0.0 -115 SP1 47 THR SC1 115 0.0 -116 P2 48 ASP BB 116 0.0 -117 SQ5n 48 ASP SC1 117 -1.0 -118 SP1 49 GLY BB 118 0.0 -119 P2 50 SER BB 119 0.0 -120 TP1 50 SER SC1 120 0.0 -121 P2 51 THR BB 121 0.0 -122 SP1 51 THR SC1 122 0.0 -123 P2 52 ASP BB 123 0.0 -124 SQ5n 52 ASP SC1 124 -1.0 -125 P2 53 TYR BB 125 0.0 -126 TC4 53 TYR SC1 126 0.0 -127 TC5 53 TYR SC2 127 0.0 -128 TC5 53 TYR SC3 128 0.0 -129 TN6 53 TYR SC4 129 0.0 -130 SP1 54 GLY BB 130 0.0 -131 P2 55 ILE BB 131 0.0 -132 SC2 55 ILE SC1 132 0.0 -133 P2 56 LEU BB 133 0.0 -134 SC2 56 LEU SC1 134 0.0 -135 P2 57 GLN BB 135 0.0 -136 P5 57 GLN SC1 136 0.0 -137 P2 58 ILE BB 137 0.0 -138 SC2 58 ILE SC1 138 0.0 -139 P2 59 ASN BB 139 0.0 -140 SP5 59 ASN SC1 140 0.0 -141 P2 60 SER BB 141 0.0 -142 TP1 60 SER SC1 142 0.0 -143 P2 61 ARG BB 143 0.0 -144 SC3 61 ARG SC1 144 0.0 -145 SQ3p 61 ARG SC2 145 1.0 -146 P2 62 TRP BB 146 0.0 -147 TC4 62 TRP SC1 147 0.0 36.0 -148 TN6d 62 TRP SC2 148 0.0 36.0 -149 TC5 62 TRP SC3 149 0.0 0.0 -150 TC5 62 TRP SC4 150 0.0 36.0 -151 TC5 62 TRP SC5 151 0.0 36.0 -152 P2 63 TRP BB 152 0.0 -153 TC4 63 TRP SC1 153 0.0 36.0 -154 TN6d 63 TRP SC2 154 0.0 36.0 -155 TC5 63 TRP SC3 155 0.0 0.0 -156 TC5 63 TRP SC4 156 0.0 36.0 -157 TC5 63 TRP SC5 157 0.0 36.0 -158 P2 64 CYS BB 158 0.0 -159 TC6 64 CYS SC1 159 0.0 -160 P2 65 ASN BB 160 0.0 -161 SP5 65 ASN SC1 161 0.0 -162 P2 66 ASP BB 162 0.0 -163 SQ5n 66 ASP SC1 163 -1.0 -164 SP1 67 GLY BB 164 0.0 -165 P2 68 ARG BB 165 0.0 -166 SC3 68 ARG SC1 166 0.0 -167 SQ3p 68 ARG SC2 167 1.0 -168 P2 69 THR BB 168 0.0 -169 SP1 69 THR SC1 169 0.0 -170 SP2a 70 PRO BB 170 0.0 -171 SC3 70 PRO SC1 171 0.0 -172 SP1 71 GLY BB 172 0.0 -173 P2 72 SER BB 173 0.0 -174 TP1 72 SER SC1 174 0.0 -175 P2 73 ARG BB 175 0.0 -176 SC3 73 ARG SC1 176 0.0 -177 SQ3p 73 ARG SC2 177 1.0 -178 P2 74 ASN BB 178 0.0 -179 SP5 74 ASN SC1 179 0.0 -180 P2 75 LEU BB 180 0.0 -181 SC2 75 LEU SC1 181 0.0 -182 P2 76 CYS BB 182 0.0 -183 TC6 76 CYS SC1 183 0.0 -184 P2 77 ASN BB 184 0.0 -185 SP5 77 ASN SC1 185 0.0 -186 P2 78 ILE BB 186 0.0 -187 SC2 78 ILE SC1 187 0.0 -188 SP2a 79 PRO BB 188 0.0 -189 SC3 79 PRO SC1 189 0.0 -190 P2 80 CYS BB 190 0.0 -191 TC6 80 CYS SC1 191 0.0 -192 P2 81 SER BB 192 0.0 -193 TP1 81 SER SC1 193 0.0 -194 SP2 82 ALA BB 194 0.0 -195 TC3 82 ALA SC1 195 0.0 -196 P2 83 LEU BB 196 0.0 -197 SC2 83 LEU SC1 197 0.0 -198 P2 84 LEU BB 198 0.0 -199 SC2 84 LEU SC1 199 0.0 -200 P2 85 SER BB 200 0.0 -201 TP1 85 SER SC1 201 0.0 -202 P2 86 SER BB 202 0.0 -203 TP1 86 SER SC1 203 0.0 -204 P2 87 ASP BB 204 0.0 -205 SQ5n 87 ASP SC1 205 -1.0 -206 P2 88 ILE BB 206 0.0 -207 SC2 88 ILE SC1 207 0.0 -208 P2 89 THR BB 208 0.0 -209 SP1 89 THR SC1 209 0.0 -210 SP2 90 ALA BB 210 0.0 -211 TC3 90 ALA SC1 211 0.0 -212 P2 91 SER BB 212 0.0 -213 TP1 91 SER SC1 213 0.0 -214 SP2 92 VAL BB 214 0.0 -215 SC3 92 VAL SC1 215 0.0 -216 P2 93 ASN BB 216 0.0 -217 SP5 93 ASN SC1 217 0.0 -218 P2 94 CYS BB 218 0.0 -219 TC6 94 CYS SC1 219 0.0 -220 SP2 95 ALA BB 220 0.0 -221 TC3 95 ALA SC1 221 0.0 -222 P2 96 LYS BB 222 0.0 -223 SC3 96 LYS SC1 223 0.0 -224 SQ4p 96 LYS SC2 224 1.0 -225 P2 97 LYS BB 225 0.0 -226 SC3 97 LYS SC1 226 0.0 -227 SQ4p 97 LYS SC2 227 1.0 -228 P2 98 ILE BB 228 0.0 -229 SC2 98 ILE SC1 229 0.0 -230 SP2 99 VAL BB 230 0.0 -231 SC3 99 VAL SC1 231 0.0 -232 P2 100 SER BB 232 0.0 -233 TP1 100 SER SC1 233 0.0 -234 P2 101 ASP BB 234 0.0 -235 SQ5n 101 ASP SC1 235 -1.0 -236 SP1 102 GLY BB 236 0.0 -237 P2 103 ASN BB 237 0.0 -238 SP5 103 ASN SC1 238 0.0 -239 SP1 104 GLY BB 239 0.0 -240 P2 105 MET BB 240 0.0 -241 C6 105 MET SC1 241 0.0 -242 P2 106 ASN BB 242 0.0 -243 SP5 106 ASN SC1 243 0.0 -244 SP2 107 ALA BB 244 0.0 -245 TC3 107 ALA SC1 245 0.0 -246 P2 108 TRP BB 246 0.0 -247 TC4 108 TRP SC1 247 0.0 36.0 -248 TN6d 108 TRP SC2 248 0.0 36.0 -249 TC5 108 TRP SC3 249 0.0 0.0 -250 TC5 108 TRP SC4 250 0.0 36.0 -251 TC5 108 TRP SC5 251 0.0 36.0 -252 SP2 109 VAL BB 252 0.0 -253 SC3 109 VAL SC1 253 0.0 -254 SP2 110 ALA BB 254 0.0 -255 TC3 110 ALA SC1 255 0.0 -256 P2 111 TRP BB 256 0.0 -257 TC4 111 TRP SC1 257 0.0 36.0 -258 TN6d 111 TRP SC2 258 0.0 36.0 -259 TC5 111 TRP SC3 259 0.0 0.0 -260 TC5 111 TRP SC4 260 0.0 36.0 -261 TC5 111 TRP SC5 261 0.0 36.0 -262 P2 112 ARG BB 262 0.0 -263 SC3 112 ARG SC1 263 0.0 -264 SQ3p 112 ARG SC2 264 1.0 -265 P2 113 ASN BB 265 0.0 -266 SP5 113 ASN SC1 266 0.0 -267 P2 114 ARG BB 267 0.0 -268 SC3 114 ARG SC1 268 0.0 -269 SQ3p 114 ARG SC2 269 1.0 -270 P2 115 CYS BB 270 0.0 -271 TC6 115 CYS SC1 271 0.0 -272 P2 116 LYS BB 272 0.0 -273 SC3 116 LYS SC1 273 0.0 -274 SQ4p 116 LYS SC2 274 1.0 -275 SP1 117 GLY BB 275 0.0 -276 P2 118 THR BB 276 0.0 -277 SP1 118 THR SC1 277 0.0 -278 P2 119 ASP BB 278 0.0 -279 SQ5n 119 ASP SC1 279 -1.0 -280 SP2 120 VAL BB 280 0.0 -281 SC3 120 VAL SC1 281 0.0 -282 P2 121 GLN BB 282 0.0 -283 P5 121 GLN SC1 283 0.0 -284 SP2 122 ALA BB 284 0.0 -285 TC3 122 ALA SC1 285 0.0 -286 P2 123 TRP BB 286 0.0 -287 TC4 123 TRP SC1 287 0.0 36.0 -288 TN6d 123 TRP SC2 288 0.0 36.0 -289 TC5 123 TRP SC3 289 0.0 0.0 -290 TC5 123 TRP SC4 290 0.0 36.0 -291 TC5 123 TRP SC5 291 0.0 36.0 -292 P2 124 ILE BB 292 0.0 -293 SC2 124 ILE SC1 293 0.0 -294 P2 125 ARG BB 294 0.0 -295 SC3 125 ARG SC1 295 0.0 -296 SQ3p 125 ARG SC2 296 1.0 -297 SP1 126 GLY BB 297 0.0 -298 P2 127 CYS BB 298 0.0 -299 TC6 127 CYS SC1 299 0.0 -300 P2 128 ARG BB 300 0.0 -301 SC3 128 ARG SC1 301 0.0 -302 SQ3p 128 ARG SC2 302 1.0 -303 Q5 129 LEU BB 303 -1 -304 SC2 129 LEU SC1 304 0.0 -305 molecule_0_1 1 LYS CA 305 0 0.0 -306 molecule_0_2 2 VAL CA 306 0 0.0 -307 molecule_0_3 3 PHE CA 307 0 0.0 -308 molecule_0_4 4 GLY CA 308 0 0.0 -309 molecule_0_5 5 ARG CA 309 0 0.0 -310 molecule_0_6 6 CYS CA 310 0 0.0 -311 molecule_0_7 7 GLU CA 311 0 0.0 -312 molecule_0_8 8 LEU CA 312 0 0.0 -313 molecule_0_9 9 ALA CA 313 0 0.0 -314 molecule_0_10 10 ALA CA 314 0 0.0 -315 molecule_0_11 11 ALA CA 315 0 0.0 -316 molecule_0_12 12 MET CA 316 0 0.0 -317 molecule_0_13 13 LYS CA 317 0 0.0 -318 molecule_0_14 14 ARG CA 318 0 0.0 -319 molecule_0_15 15 HIS CA 319 0 0.0 -320 molecule_0_16 16 GLY CA 320 0 0.0 -321 molecule_0_17 17 LEU CA 321 0 0.0 -322 molecule_0_18 18 ASP CA 322 0 0.0 -323 molecule_0_19 19 ASN CA 323 0 0.0 -324 molecule_0_20 20 TYR CA 324 0 0.0 -325 molecule_0_21 21 ARG CA 325 0 0.0 -326 molecule_0_22 22 GLY CA 326 0 0.0 -327 molecule_0_23 23 TYR CA 327 0 0.0 -328 molecule_0_24 24 SER CA 328 0 0.0 -329 molecule_0_25 25 LEU CA 329 0 0.0 -330 molecule_0_26 26 GLY CA 330 0 0.0 -331 molecule_0_27 27 ASN CA 331 0 0.0 -332 molecule_0_28 28 TRP CA 332 0 0.0 -333 molecule_0_29 29 VAL CA 333 0 0.0 -334 molecule_0_30 30 CYS CA 334 0 0.0 -335 molecule_0_31 31 ALA CA 335 0 0.0 -336 molecule_0_32 32 ALA CA 336 0 0.0 -337 molecule_0_33 33 LYS CA 337 0 0.0 -338 molecule_0_34 34 PHE CA 338 0 0.0 -339 molecule_0_35 35 GLU CA 339 0 0.0 -340 molecule_0_36 36 SER CA 340 0 0.0 -341 molecule_0_37 37 ASN CA 341 0 0.0 -342 molecule_0_38 38 PHE CA 342 0 0.0 -343 molecule_0_39 39 ASN CA 343 0 0.0 -344 molecule_0_40 40 THR CA 344 0 0.0 -345 molecule_0_41 41 GLN CA 345 0 0.0 -346 molecule_0_42 42 ALA CA 346 0 0.0 -347 molecule_0_43 43 THR CA 347 0 0.0 -348 molecule_0_44 44 ASN CA 348 0 0.0 -349 molecule_0_45 45 ARG CA 349 0 0.0 -350 molecule_0_46 46 ASN CA 350 0 0.0 -351 molecule_0_47 47 THR CA 351 0 0.0 -352 molecule_0_48 48 ASP CA 352 0 0.0 -353 molecule_0_49 49 GLY CA 353 0 0.0 -354 molecule_0_50 50 SER CA 354 0 0.0 -355 molecule_0_51 51 THR CA 355 0 0.0 -356 molecule_0_52 52 ASP CA 356 0 0.0 -357 molecule_0_53 53 TYR CA 357 0 0.0 -358 molecule_0_54 54 GLY CA 358 0 0.0 -359 molecule_0_55 55 ILE CA 359 0 0.0 -360 molecule_0_56 56 LEU CA 360 0 0.0 -361 molecule_0_57 57 GLN CA 361 0 0.0 -362 molecule_0_58 58 ILE CA 362 0 0.0 -363 molecule_0_59 59 ASN CA 363 0 0.0 -364 molecule_0_60 60 SER CA 364 0 0.0 -365 molecule_0_61 61 ARG CA 365 0 0.0 -366 molecule_0_62 62 TRP CA 366 0 0.0 -367 molecule_0_63 63 TRP CA 367 0 0.0 -368 molecule_0_64 64 CYS CA 368 0 0.0 -369 molecule_0_65 65 ASN CA 369 0 0.0 -370 molecule_0_66 66 ASP CA 370 0 0.0 -371 molecule_0_67 67 GLY CA 371 0 0.0 -372 molecule_0_68 68 ARG CA 372 0 0.0 -373 molecule_0_69 69 THR CA 373 0 0.0 -374 molecule_0_70 70 PRO CA 374 0 0.0 -375 molecule_0_71 71 GLY CA 375 0 0.0 -376 molecule_0_72 72 SER CA 376 0 0.0 -377 molecule_0_73 73 ARG CA 377 0 0.0 -378 molecule_0_74 74 ASN CA 378 0 0.0 -379 molecule_0_75 75 LEU CA 379 0 0.0 -380 molecule_0_76 76 CYS CA 380 0 0.0 -381 molecule_0_77 77 ASN CA 381 0 0.0 -382 molecule_0_78 78 ILE CA 382 0 0.0 -383 molecule_0_79 79 PRO CA 383 0 0.0 -384 molecule_0_80 80 CYS CA 384 0 0.0 -385 molecule_0_81 81 SER CA 385 0 0.0 -386 molecule_0_82 82 ALA CA 386 0 0.0 -387 molecule_0_83 83 LEU CA 387 0 0.0 -388 molecule_0_84 84 LEU CA 388 0 0.0 -389 molecule_0_85 85 SER CA 389 0 0.0 -390 molecule_0_86 86 SER CA 390 0 0.0 -391 molecule_0_87 87 ASP CA 391 0 0.0 -392 molecule_0_88 88 ILE CA 392 0 0.0 -393 molecule_0_89 89 THR CA 393 0 0.0 -394 molecule_0_90 90 ALA CA 394 0 0.0 -395 molecule_0_91 91 SER CA 395 0 0.0 -396 molecule_0_92 92 VAL CA 396 0 0.0 -397 molecule_0_93 93 ASN CA 397 0 0.0 -398 molecule_0_94 94 CYS CA 398 0 0.0 -399 molecule_0_95 95 ALA CA 399 0 0.0 -400 molecule_0_96 96 LYS CA 400 0 0.0 -401 molecule_0_97 97 LYS CA 401 0 0.0 -402 molecule_0_98 98 ILE CA 402 0 0.0 -403 molecule_0_99 99 VAL CA 403 0 0.0 -404 molecule_0_100 100 SER CA 404 0 0.0 -405 molecule_0_101 101 ASP CA 405 0 0.0 -406 molecule_0_102 102 GLY CA 406 0 0.0 -407 molecule_0_103 103 ASN CA 407 0 0.0 -408 molecule_0_104 104 GLY CA 408 0 0.0 -409 molecule_0_105 105 MET CA 409 0 0.0 -410 molecule_0_106 106 ASN CA 410 0 0.0 -411 molecule_0_107 107 ALA CA 411 0 0.0 -412 molecule_0_108 108 TRP CA 412 0 0.0 -413 molecule_0_109 109 VAL CA 413 0 0.0 -414 molecule_0_110 110 ALA CA 414 0 0.0 -415 molecule_0_111 111 TRP CA 415 0 0.0 -416 molecule_0_112 112 ARG CA 416 0 0.0 -417 molecule_0_113 113 ASN CA 417 0 0.0 -418 molecule_0_114 114 ARG CA 418 0 0.0 -419 molecule_0_115 115 CYS CA 419 0 0.0 -420 molecule_0_116 116 LYS CA 420 0 0.0 -421 molecule_0_117 117 GLY CA 421 0 0.0 -422 molecule_0_118 118 THR CA 422 0 0.0 -423 molecule_0_119 119 ASP CA 423 0 0.0 -424 molecule_0_120 120 VAL CA 424 0 0.0 -425 molecule_0_121 121 GLN CA 425 0 0.0 -426 molecule_0_122 122 ALA CA 426 0 0.0 -427 molecule_0_123 123 TRP CA 427 0 0.0 -428 molecule_0_124 124 ILE CA 428 0 0.0 -429 molecule_0_125 125 ARG CA 429 0 0.0 -430 molecule_0_126 126 GLY CA 430 0 0.0 -431 molecule_0_127 127 CYS CA 431 0 0.0 -432 molecule_0_128 128 ARG CA 432 0 0.0 -433 molecule_0_129 129 LEU CA 433 0 0.0 - -[ bonds ] -; Backbone bonds - 1 4 1 0.350 4000 - 4 6 1 0.350 4000 - 6 10 1 0.350 4000 - 34 38 1 0.350 4000 - 38 39 1 0.350 4000 - 39 41 1 0.350 4000 - 41 43 1 0.350 4000 - 43 45 1 0.350 4000 - 45 50 1 0.350 4000 - 50 53 1 0.350 4000 - 53 54 1 0.350 4000 - 54 59 1 0.350 4000 - 91 93 1 0.350 4000 - 93 97 1 0.350 4000 - 97 99 1 0.350 4000 - 99 101 1 0.350 4000 -101 103 1 0.350 4000 -103 105 1 0.350 4000 -105 107 1 0.350 4000 -107 109 1 0.350 4000 -109 112 1 0.350 4000 -112 114 1 0.350 4000 -114 116 1 0.350 4000 -116 118 1 0.350 4000 -118 119 1 0.350 4000 -119 121 1 0.350 4000 -121 123 1 0.350 4000 -123 125 1 0.350 4000 -125 130 1 0.350 4000 -130 131 1 0.350 4000 -131 133 1 0.350 4000 -133 135 1 0.350 4000 -135 137 1 0.350 4000 -137 139 1 0.350 4000 -139 141 1 0.350 4000 -141 143 1 0.350 4000 -143 146 1 0.350 4000 -146 152 1 0.350 4000 -152 158 1 0.350 4000 -158 160 1 0.350 4000 -160 162 1 0.350 4000 -162 164 1 0.350 4000 -164 165 1 0.350 4000 -165 168 1 0.350 4000 -168 170 1 0.350 4000 -170 172 1 0.350 4000 -172 173 1 0.350 4000 -173 175 1 0.350 4000 -175 178 1 0.350 4000 -178 180 1 0.350 4000 -180 182 1 0.350 4000 -182 184 1 0.350 4000 -184 186 1 0.350 4000 -186 188 1 0.350 4000 -200 202 1 0.350 4000 -202 204 1 0.350 4000 -204 206 1 0.350 4000 -234 236 1 0.350 4000 -236 237 1 0.350 4000 -270 272 1 0.350 4000 -272 275 1 0.350 4000 -275 276 1 0.350 4000 -276 278 1 0.350 4000 -294 297 1 0.350 4000 -297 298 1 0.350 4000 -298 300 1 0.350 4000 -300 303 1 0.350 4000 - -; Side chain bonds - 1 2 1 0.330 5000 - 2 3 1 0.360 5000 - 6 7 1 0.325 7500 - 11 12 1 0.330 5000 - 12 13 1 0.380 5000 - 14 15 1 0.341 7500 - 16 17 1 0.400 5000 - 18 19 1 0.363 7500 - 26 27 1 0.40 2500 - 28 29 1 0.330 5000 - 29 30 1 0.360 5000 - 31 32 1 0.330 5000 - 32 33 1 0.380 5000 - 34 35 1 0.336 7500 - 39 40 1 0.363 7500 - 41 42 1 0.352 7500 - 43 44 1 0.352 5000 - 45 46 1 0.325 5000 - 50 51 1 0.330 5000 - 51 52 1 0.380 5000 - 54 55 1 0.325 5000 - 59 60 1 0.287 7500 - 61 62 1 0.363 7500 - 64 65 1 0.352 5000 - 66 67 1 0.315 5000 - 74 75 1 0.341 7500 - 80 81 1 0.330 5000 - 81 82 1 0.360 5000 - 83 84 1 0.325 7500 - 87 88 1 0.400 5000 - 89 90 1 0.287 7500 - 91 92 1 0.352 5000 - 93 94 1 0.325 7500 - 97 98 1 0.352 5000 -101 102 1 0.400 5000 -107 108 1 0.352 5000 -109 110 1 0.330 5000 -110 111 1 0.380 5000 -112 113 1 0.352 5000 -116 117 1 0.352 7500 -119 120 1 0.287 7500 -123 124 1 0.352 7500 -125 126 1 0.325 5000 -133 134 1 0.363 7500 -135 136 1 0.400 5000 -139 140 1 0.352 5000 -141 142 1 0.287 7500 -143 144 1 0.330 5000 -144 145 1 0.380 5000 -146 147 1 0.315 5000 -152 153 1 0.315 5000 -158 159 1 0.341 7500 -160 161 1 0.352 5000 -162 163 1 0.352 7500 -165 166 1 0.330 5000 -166 167 1 0.380 5000 -170 171 1 0.330 7500 -173 174 1 0.287 7500 -175 176 1 0.330 5000 -176 177 1 0.380 5000 -178 179 1 0.352 5000 -180 181 1 0.363 7500 -182 183 1 0.341 7500 -184 185 1 0.352 5000 -188 189 1 0.330 7500 -190 191 1 0.341 7500 -192 193 1 0.287 7500 -196 197 1 0.363 7500 -198 199 1 0.363 7500 -200 201 1 0.287 7500 -202 203 1 0.287 7500 -204 205 1 0.352 7500 -212 213 1 0.287 7500 -216 217 1 0.352 5000 -218 219 1 0.341 7500 -222 223 1 0.330 5000 -223 224 1 0.360 5000 -225 226 1 0.330 5000 -226 227 1 0.360 5000 -232 233 1 0.287 7500 -234 235 1 0.352 7500 -237 238 1 0.352 5000 -240 241 1 0.40 2500 -242 243 1 0.352 5000 -246 247 1 0.315 5000 -256 257 1 0.315 5000 -262 263 1 0.330 5000 -263 264 1 0.380 5000 -265 266 1 0.352 5000 -267 268 1 0.330 5000 -268 269 1 0.380 5000 -270 271 1 0.341 7500 -272 273 1 0.330 5000 -273 274 1 0.360 5000 -278 279 1 0.352 7500 -282 283 1 0.400 5000 -286 287 1 0.315 5000 -294 295 1 0.330 5000 -295 296 1 0.380 5000 -298 299 1 0.341 7500 -300 301 1 0.330 5000 -301 302 1 0.380 5000 -303 304 1 0.363 7500 - -#ifdef FLEXIBLE -; Side chain bonds - 4 5 1 0.292 1000000 - 7 8 1 0.340 1000000 - 7 9 1 0.340 1000000 - 8 9 1 0.290 1000000 - 20 21 1 0.270 1000000 - 22 23 1 0.270 1000000 - 24 25 1 0.270 1000000 - 35 36 1 0.320 1000000 - 35 37 1 0.300 1000000 - 36 37 1 0.270 1000000 - 46 47 1 0.300 1000000 - 46 48 1 0.300 1000000 - 47 49 1 0.285 1000000 - 48 49 1 0.285 1000000 - 47 48 1 0.300 1000000 - 55 56 1 0.300 1000000 - 55 57 1 0.300 1000000 - 56 58 1 0.285 1000000 - 57 58 1 0.285 1000000 - 56 57 1 0.300 1000000 - 67 68 1 0.335 1000000 - 68 71 1 0.412 1000000 - 70 71 1 0.293 1000000 - 67 70 1 0.404 1000000 - 68 70 1 0.470 1000000 - 72 73 1 0.292 1000000 - 76 77 1 0.270 1000000 - 78 79 1 0.270 1000000 - 84 85 1 0.340 1000000 - 84 86 1 0.340 1000000 - 85 86 1 0.290 1000000 - 94 95 1 0.340 1000000 - 94 96 1 0.340 1000000 - 95 96 1 0.290 1000000 - 99 100 1 0.305 1000000 -103 104 1 0.270 1000000 -105 106 1 0.305 1000000 -114 115 1 0.305 1000000 -121 122 1 0.305 1000000 -126 127 1 0.300 1000000 -126 128 1 0.300 1000000 -127 129 1 0.285 1000000 -128 129 1 0.285 1000000 -127 128 1 0.300 1000000 -131 132 1 0.341 1000000 -137 138 1 0.341 1000000 -147 148 1 0.335 1000000 -148 151 1 0.412 1000000 -150 151 1 0.293 1000000 -147 150 1 0.404 1000000 -148 150 1 0.470 1000000 -153 154 1 0.335 1000000 -154 157 1 0.412 1000000 -156 157 1 0.293 1000000 -153 156 1 0.404 1000000 -154 156 1 0.470 1000000 -168 169 1 0.305 1000000 -186 187 1 0.341 1000000 -194 195 1 0.270 1000000 -206 207 1 0.341 1000000 -208 209 1 0.305 1000000 -210 211 1 0.270 1000000 -214 215 1 0.292 1000000 -220 221 1 0.270 1000000 -228 229 1 0.341 1000000 -230 231 1 0.292 1000000 -244 245 1 0.270 1000000 -247 248 1 0.335 1000000 -248 251 1 0.412 1000000 -250 251 1 0.293 1000000 -247 250 1 0.404 1000000 -248 250 1 0.470 1000000 -252 253 1 0.292 1000000 -254 255 1 0.270 1000000 -257 258 1 0.335 1000000 -258 261 1 0.412 1000000 -260 261 1 0.293 1000000 -257 260 1 0.404 1000000 -258 260 1 0.470 1000000 -276 277 1 0.305 1000000 -280 281 1 0.292 1000000 -284 285 1 0.270 1000000 -287 288 1 0.335 1000000 -288 291 1 0.412 1000000 -290 291 1 0.293 1000000 -287 290 1 0.404 1000000 -288 290 1 0.470 1000000 -292 293 1 0.341 1000000 -#endif - -[ constraints ] -; Backbone bonds - 10 11 1 0.33 - 11 14 1 0.310 - 14 16 1 0.310 - 16 18 1 0.310 - 18 20 1 0.310 - 20 22 1 0.310 - 22 24 1 0.310 - 24 26 1 0.310 - 26 28 1 0.310 - 28 31 1 0.310 - 31 34 1 0.33 - 59 61 1 0.33 - 61 63 1 0.310 - 63 64 1 0.310 - 64 66 1 0.310 - 66 72 1 0.310 - 72 74 1 0.310 - 74 76 1 0.310 - 76 78 1 0.310 - 78 80 1 0.310 - 80 83 1 0.310 - 83 87 1 0.310 - 87 89 1 0.310 - 89 91 1 0.33 -188 190 1 0.33 -190 192 1 0.310 -192 194 1 0.310 -194 196 1 0.310 -196 198 1 0.310 -198 200 1 0.33 -206 208 1 0.33 -208 210 1 0.310 -210 212 1 0.310 -212 214 1 0.310 -214 216 1 0.310 -216 218 1 0.310 -218 220 1 0.310 -220 222 1 0.310 -222 225 1 0.310 -225 228 1 0.310 -228 230 1 0.310 -230 232 1 0.310 -232 234 1 0.33 -237 239 1 0.33 -239 240 1 0.310 -240 242 1 0.310 -242 244 1 0.310 -244 246 1 0.33 -246 252 1 0.33 -252 254 1 0.310 -254 256 1 0.310 -256 262 1 0.310 -262 265 1 0.310 -265 267 1 0.310 -267 270 1 0.33 -278 280 1 0.33 -280 282 1 0.310 -282 284 1 0.310 -284 286 1 0.310 -286 292 1 0.310 -292 294 1 0.33 - -#ifndef FLEXIBLE -; Side chain bonds - 4 5 1 0.292 - 7 8 1 0.340 - 7 9 1 0.340 - 8 9 1 0.290 - 20 21 1 0.270 - 22 23 1 0.270 - 24 25 1 0.270 - 35 36 1 0.320 - 35 37 1 0.300 - 36 37 1 0.270 - 46 47 1 0.300 - 46 48 1 0.300 - 47 49 1 0.285 - 48 49 1 0.285 - 47 48 1 0.300 - 55 56 1 0.300 - 55 57 1 0.300 - 56 58 1 0.285 - 57 58 1 0.285 - 56 57 1 0.300 - 67 68 1 0.335 - 68 71 1 0.412 - 70 71 1 0.293 - 67 70 1 0.404 - 68 70 1 0.470 - 72 73 1 0.292 - 76 77 1 0.270 - 78 79 1 0.270 - 84 85 1 0.340 - 84 86 1 0.340 - 85 86 1 0.290 - 94 95 1 0.340 - 94 96 1 0.340 - 95 96 1 0.290 - 99 100 1 0.305 -103 104 1 0.270 -105 106 1 0.305 -114 115 1 0.305 -121 122 1 0.305 -126 127 1 0.300 -126 128 1 0.300 -127 129 1 0.285 -128 129 1 0.285 -127 128 1 0.300 -131 132 1 0.341 -137 138 1 0.341 -147 148 1 0.335 -148 151 1 0.412 -150 151 1 0.293 -147 150 1 0.404 -148 150 1 0.470 -153 154 1 0.335 -154 157 1 0.412 -156 157 1 0.293 -153 156 1 0.404 -154 156 1 0.470 -168 169 1 0.305 -186 187 1 0.341 -194 195 1 0.270 -206 207 1 0.341 -208 209 1 0.305 -210 211 1 0.270 -214 215 1 0.292 -220 221 1 0.270 -228 229 1 0.341 -230 231 1 0.292 -244 245 1 0.270 -247 248 1 0.335 -248 251 1 0.412 -250 251 1 0.293 -247 250 1 0.404 -248 250 1 0.470 -252 253 1 0.292 -254 255 1 0.270 -257 258 1 0.335 -258 261 1 0.412 -260 261 1 0.293 -257 260 1 0.404 -258 260 1 0.470 -276 277 1 0.305 -280 281 1 0.292 -284 285 1 0.270 -287 288 1 0.335 -288 291 1 0.412 -290 291 1 0.293 -287 290 1 0.404 -288 290 1 0.470 -292 293 1 0.341 -#endif - -[ angles ] -; BBB angles - 6 10 11 10 127 20 - 10 11 14 10 127 20 - 11 14 16 2 96 700 - 14 16 18 2 96 700 - 16 18 20 2 96 700 - 18 20 22 2 96 700 - 20 22 24 2 96 700 - 22 24 26 2 96 700 - 24 26 28 2 96 700 - 26 28 31 2 96 700 - 28 31 34 10 100 20 - 31 34 38 10 100 20 - 54 59 61 10 127 20 - 59 61 63 10 127 20 - 61 63 64 2 96 700 - 63 64 66 2 96 700 - 64 66 72 2 96 700 - 66 72 74 2 96 700 - 72 74 76 2 96 700 - 74 76 78 2 96 700 - 76 78 80 2 96 700 - 78 80 83 2 96 700 - 80 83 87 2 96 700 - 83 87 89 2 96 700 - 87 89 91 10 100 20 - 89 91 93 10 100 20 -186 188 190 10 130 20 -188 190 192 10 134 25 -190 192 194 2 96 700 -192 194 196 2 96 700 -194 196 198 2 96 700 -196 198 200 10 130 20 -198 200 202 10 130 20 -204 206 208 10 127 20 -206 208 210 10 127 20 -208 210 212 2 96 700 -210 212 214 2 96 700 -212 214 216 2 96 700 -214 216 218 2 96 700 -216 218 220 2 96 700 -218 220 222 2 96 700 -220 222 225 2 96 700 -222 225 228 2 96 700 -225 228 230 2 96 700 -228 230 232 2 96 700 -230 232 234 10 100 20 -232 234 236 10 100 20 -236 237 239 10 130 20 -237 239 240 10 130 20 -239 240 242 2 96 700 -240 242 244 2 96 700 -242 244 246 10 130 20 -244 246 252 10 130 20 -246 252 254 10 130 20 -252 254 256 2 96 700 -254 256 262 2 96 700 -256 262 265 2 96 700 -262 265 267 2 96 700 -265 267 270 10 100 20 -267 270 272 10 100 20 -276 278 280 10 127 20 -278 280 282 10 127 20 -280 282 284 2 96 700 -282 284 286 2 96 700 -284 286 292 2 96 700 -286 292 294 10 100 20 -292 294 297 10 100 20 - 1 4 6 10 127 20 - 4 6 10 10 127 20 - 41 43 45 10 100 20 - 43 45 50 10 100 20 - 45 50 53 10 100 20 - 50 53 54 10 100 20 - 53 54 59 10 100 20 - 91 93 97 10 100 20 - 93 97 99 10 100 20 - 97 99 101 10 100 20 -101 103 105 10 100 20 -103 105 107 10 127 20 -105 107 109 10 134 25 -107 109 112 10 127 20 -109 112 114 10 100 20 -118 119 121 10 127 20 -119 121 123 10 127 20 -121 123 125 10 134 25 -123 125 130 10 100 20 -125 130 131 10 100 20 -133 135 137 10 100 20 -135 137 139 10 100 20 -137 139 141 10 100 20 -139 141 143 10 100 20 -152 158 160 10 100 20 -158 160 162 10 127 20 -160 162 164 10 127 20 -184 186 188 10 127 20 -165 168 170 10 127 20 -168 170 172 10 100 20 -170 172 173 10 100 20 -114 116 118 10 100 20 -116 118 119 10 100 20 -162 164 165 10 127 20 -164 165 168 10 127 20 -182 184 186 10 100 20 -200 202 204 10 130 20 -202 204 206 10 127 20 -234 236 237 10 100 20 -272 275 276 10 100 20 -275 276 278 10 100 20 - 34 38 39 10 100 20 - 38 39 41 10 100 20 - 39 41 43 10 100 20 - 99 101 103 10 100 20 -112 114 116 10 100 20 -146 152 158 10 100 20 -172 173 175 10 100 20 -173 175 178 10 127 20 -175 178 180 10 100 20 -178 180 182 10 100 20 -180 182 184 10 100 20 -294 297 298 10 100 20 -297 298 300 10 100 20 -298 300 303 10 127 20 -130 131 133 10 100 20 -131 133 135 10 100 20 -141 143 146 10 100 20 -143 146 152 10 100 20 -270 272 275 10 100 20 - -; BBS angles regular martini - 1 4 5 2 100 25 - 4 6 7 2 100 25 - 10 11 12 2 100 25 - 11 14 15 2 100 25 - 14 16 17 2 100 25 - 16 18 19 2 100 25 - 18 20 21 2 100 25 - 20 22 23 2 100 25 - 22 24 25 2 100 25 - 24 26 27 2 100 25 - 26 28 29 2 100 25 - 28 31 32 2 100 25 - 31 34 35 2 100 25 - 38 39 40 2 100 25 - 39 41 42 2 100 25 - 41 43 44 2 100 25 - 43 45 46 2 100 25 - 45 50 51 2 100 25 - 53 54 55 2 100 25 - 54 59 60 2 100 25 - 59 61 62 2 100 25 - 63 64 65 2 100 25 - 64 66 67 2 100 25 - 66 72 73 2 100 25 - 72 74 75 2 100 25 - 74 76 77 2 100 25 - 76 78 79 2 100 25 - 78 80 81 2 100 25 - 80 83 84 2 100 25 - 83 87 88 2 100 25 - 87 89 90 2 100 25 - 89 91 92 2 100 25 - 91 93 94 2 100 25 - 93 97 98 2 100 25 - 97 99 100 2 100 25 - 99 101 102 2 100 25 -101 103 104 2 100 25 -103 105 106 2 100 25 -105 107 108 2 100 25 -107 109 110 2 100 25 -109 112 113 2 100 25 -112 114 115 2 100 25 -114 116 117 2 100 25 -118 119 120 2 100 25 -119 121 122 2 100 25 -121 123 124 2 100 25 -123 125 126 2 100 25 -130 131 132 2 100 25 -131 133 134 2 100 25 -133 135 136 2 100 25 -135 137 138 2 100 25 -137 139 140 2 100 25 -139 141 142 2 100 25 -141 143 144 2 100 25 -143 146 147 2 100 25 -146 152 153 2 100 25 -152 158 159 2 100 25 -158 160 161 2 100 25 -160 162 163 2 100 25 -164 165 166 2 100 25 -165 168 169 2 100 25 -168 170 171 2 100 25 -172 173 174 2 100 25 -173 175 176 2 100 25 -175 178 179 2 100 25 -178 180 181 2 100 25 -180 182 183 2 100 25 -182 184 185 2 100 25 -184 186 187 2 100 25 -186 188 189 2 100 25 -188 190 191 2 100 25 -190 192 193 2 100 25 -192 194 195 2 100 25 -194 196 197 2 100 25 -196 198 199 2 100 25 -198 200 201 2 100 25 -200 202 203 2 100 25 -202 204 205 2 100 25 -204 206 207 2 100 25 -206 208 209 2 100 25 -208 210 211 2 100 25 -210 212 213 2 100 25 -212 214 215 2 100 25 -214 216 217 2 100 25 -216 218 219 2 100 25 -218 220 221 2 100 25 -220 222 223 2 100 25 -222 225 226 2 100 25 -225 228 229 2 100 25 -228 230 231 2 100 25 -230 232 233 2 100 25 -232 234 235 2 100 25 -236 237 238 2 100 25 -239 240 241 2 100 25 -240 242 243 2 100 25 -242 244 245 2 100 25 -244 246 247 2 100 25 -246 252 253 2 100 25 -252 254 255 2 100 25 -254 256 257 2 100 25 -256 262 263 2 100 25 -262 265 266 2 100 25 -265 267 268 2 100 25 -267 270 271 2 100 25 -270 272 273 2 100 25 -275 276 277 2 100 25 -276 278 279 2 100 25 -278 280 281 2 100 25 -280 282 283 2 100 25 -282 284 285 2 100 25 -284 286 287 2 100 25 -286 292 293 2 100 25 -292 294 295 2 100 25 -297 298 299 2 100 25 -298 300 301 2 100 25 -300 303 304 2 100 25 - -; First SBB regular martini - 2 1 4 2 100 25 - -; Side chain angles - 1 2 3 2 180.000 25.0 - 6 7 8 2 120.000 50.0 - 6 7 9 2 120.000 50.0 - 11 12 13 2 180.000 25.0 - 28 29 30 2 180.000 25.0 - 31 32 33 2 180.000 25.0 - 34 35 36 2 120.000 50.0 - 34 35 37 2 120.000 50.0 - 45 46 47 2 120.000 60.0 - 45 46 48 2 120.000 60.0 - 50 51 52 2 180.000 25.0 - 54 55 56 2 120.000 60.0 - 54 55 57 2 120.000 60.0 - 66 67 68 2 120.000 60.0 - 66 67 70 2 130.000 60.0 - 80 81 82 2 180.000 25.0 - 83 84 85 2 120.000 50.0 - 83 84 86 2 120.000 50.0 - 93 94 95 2 120.000 50.0 - 93 94 96 2 120.000 50.0 -109 110 111 2 180.000 25.0 -125 126 127 2 120.000 60.0 -125 126 128 2 120.000 60.0 -143 144 145 2 180.000 25.0 -146 147 148 2 120.000 60.0 -146 147 150 2 130.000 60.0 -152 153 154 2 120.000 60.0 -152 153 156 2 130.000 60.0 -165 166 167 2 180.000 25.0 -175 176 177 2 180.000 25.0 -222 223 224 2 180.000 25.0 -225 226 227 2 180.000 25.0 -246 247 248 2 120.000 60.0 -246 247 250 2 130.000 60.0 -256 257 258 2 120.000 60.0 -256 257 260 2 130.000 60.0 -262 263 264 2 180.000 25.0 -267 268 269 2 180.000 25.0 -272 273 274 2 180.000 25.0 -286 287 288 2 120.000 60.0 -286 287 290 2 130.000 60.0 -294 295 296 2 180.000 25.0 -300 301 302 2 180.000 25.0 - -[ dihedrals ] - 11 14 16 18 1 -120 400 1 - 14 16 18 20 1 -120 400 1 - 16 18 20 22 1 -120 400 1 - 18 20 22 24 1 -120 400 1 - 20 22 24 26 1 -120 400 1 - 22 24 26 28 1 -120 400 1 - 24 26 28 31 1 -120 400 1 - 61 63 64 66 1 -120 400 1 - 63 64 66 72 1 -120 400 1 - 64 66 72 74 1 -120 400 1 - 66 72 74 76 1 -120 400 1 - 72 74 76 78 1 -120 400 1 - 74 76 78 80 1 -120 400 1 - 76 78 80 83 1 -120 400 1 - 78 80 83 87 1 -120 400 1 - 80 83 87 89 1 -120 400 1 -190 192 194 196 1 -120 400 1 -192 194 196 198 1 -120 400 1 -208 210 212 214 1 -120 400 1 -210 212 214 216 1 -120 400 1 -212 214 216 218 1 -120 400 1 -214 216 218 220 1 -120 400 1 -216 218 220 222 1 -120 400 1 -218 220 222 225 1 -120 400 1 -220 222 225 228 1 -120 400 1 -222 225 228 230 1 -120 400 1 -225 228 230 232 1 -120 400 1 -239 240 242 244 1 -120 400 1 -252 254 256 262 1 -120 400 1 -254 256 262 265 1 -120 400 1 -256 262 265 267 1 -120 400 1 -280 282 284 286 1 -120 400 1 -282 284 286 292 1 -120 400 1 - -[ exclusions ] - 6 7 8 9 - 7 8 9 - 8 9 - 34 35 36 37 - 35 36 37 - 36 37 - 45 46 47 48 49 - 46 47 48 49 - 47 48 49 - 48 49 - 54 55 56 57 58 - 55 56 57 58 - 56 57 58 - 57 58 - 66 67 68 69 70 71 - 67 68 69 70 71 - 68 69 70 71 - 69 70 71 - 70 71 - 83 84 85 86 - 84 85 86 - 85 86 - 93 94 95 96 - 94 95 96 - 95 96 -125 126 127 128 129 -126 127 128 129 -127 128 129 -128 129 -146 147 148 149 150 151 -147 148 149 150 151 -148 149 150 151 -149 150 151 -150 151 -152 153 154 155 156 157 -153 154 155 156 157 -154 155 156 157 -155 156 157 -156 157 -246 247 248 249 250 251 -247 248 249 250 251 -248 249 250 251 -249 250 251 -250 251 -256 257 258 259 260 261 -257 258 259 260 261 -258 259 260 261 -259 260 261 -260 261 -286 287 288 289 290 291 -287 288 289 290 291 -288 289 290 291 -289 290 291 -290 291 - -; Go model exclusion - 16 6 - 18 6 - 18 10 - 20 11 - 22 14 - 24 16 - 26 18 - 28 20 - 31 22 - 34 24 - 38 26 - 39 26 - 41 28 - 45 38 - 54 43 - 59 41 - 59 43 - 61 20 - 61 26 - 61 28 - 61 41 - 64 53 - 64 54 - 66 26 - 66 39 - 66 54 - 66 59 - 72 11 - 72 20 - 72 26 - 72 61 - 74 63 - 76 64 - 78 18 - 78 66 - 80 72 - 83 74 - 87 76 - 89 78 - 91 78 - 91 80 - 93 1 - 93 4 - 93 6 - 93 11 - 93 18 - 93 72 - 93 78 - 93 80 - 97 1 - 97 4 - 99 1 - 99 6 -101 1 -103 89 -107 87 -118 109 -119 109 -119 112 -121 105 -121 107 -121 109 -121 112 -123 105 -123 107 -123 112 -125 103 -125 105 -130 89 -130 99 -130 103 -131 6 -131 18 -131 78 -131 87 -131 89 -131 93 -131 97 -131 99 -133 76 -133 78 -133 87 -135 87 -135 89 -135 103 -135 105 -135 107 -135 123 -135 125 -137 123 -137 125 -139 112 -139 119 -139 121 -139 123 -141 119 -141 121 -141 125 -143 116 -143 119 -152 137 -152 139 -158 125 -158 141 -162 121 -162 141 -165 121 -168 118 -168 119 -168 141 -168 143 -170 143 -173 141 -173 143 -173 158 -175 143 -175 146 -178 146 -178 152 -178 158 -178 160 -180 146 -180 152 -182 152 -186 152 -186 158 -186 160 -186 178 -188 158 -188 160 -190 125 -190 141 -190 158 -190 160 -190 162 -194 186 -196 125 -196 130 -196 137 -196 158 -196 186 -198 99 -198 101 -198 103 -198 105 -198 125 -198 130 -200 99 -200 192 -202 1 -202 6 -202 99 -206 18 -206 24 -206 26 -206 34 -206 99 -206 131 -208 31 -208 34 -210 186 -210 194 -210 196 -212 131 -212 137 -212 196 -214 34 -214 39 -214 206 -216 208 -218 137 -218 152 -218 182 -218 186 -218 196 -218 210 -220 66 -220 133 -220 137 -220 212 -222 34 -222 38 -222 39 -222 45 -222 214 -225 152 -225 182 -225 216 -228 137 -228 152 -228 218 -230 45 -230 50 -230 54 -230 220 -232 45 -232 50 -232 222 -234 225 -239 54 -239 230 -240 54 -240 64 -240 66 -240 76 -240 230 -244 228 -246 66 -246 87 -246 133 -246 135 -246 228 -246 230 -254 83 -254 87 -256 64 -256 76 -256 240 -256 242 -262 242 -262 244 -262 246 -265 252 -267 83 -267 254 -270 74 -270 76 -270 83 -270 254 -270 256 -272 242 -272 256 -272 262 -276 267 -280 59 -280 63 -280 64 -280 74 -280 270 -284 11 -286 11 -286 63 -286 72 -286 74 -286 80 -286 276 -292 11 -292 20 -292 61 -292 63 -292 72 -294 11 -294 282 -298 11 -298 14 -303 20 -303 22 -303 28 -303 292 - -[ dihedrals ] - 49 47 48 46 2 180.0 50.0 - 58 56 57 55 2 180.0 50.0 - 71 70 68 67 2 180.0 100.0 -129 127 128 126 2 180.0 50.0 -151 150 148 147 2 180.0 100.0 -157 156 154 153 2 180.0 100.0 -251 250 248 247 2 180.0 100.0 -261 260 258 257 2 180.0 100.0 -291 290 288 287 2 180.0 100.0 - -[ virtual_sitesn ] - 69 2 71 70 68 67 -149 2 151 150 148 147 -155 2 157 156 154 153 -249 2 251 250 248 247 -259 2 261 260 258 257 -289 2 291 290 288 287 - -; Virtual go site -305 1 1 -306 1 4 -307 1 6 -308 1 10 -309 1 11 -310 1 14 -311 1 16 -312 1 18 -313 1 20 -314 1 22 -315 1 24 -316 1 26 -317 1 28 -318 1 31 -319 1 34 -320 1 38 -321 1 39 -322 1 41 -323 1 43 -324 1 45 -325 1 50 -326 1 53 -327 1 54 -328 1 59 -329 1 61 -330 1 63 -331 1 64 -332 1 66 -333 1 72 -334 1 74 -335 1 76 -336 1 78 -337 1 80 -338 1 83 -339 1 87 -340 1 89 -341 1 91 -342 1 93 -343 1 97 -344 1 99 -345 1 101 -346 1 103 -347 1 105 -348 1 107 -349 1 109 -350 1 112 -351 1 114 -352 1 116 -353 1 118 -354 1 119 -355 1 121 -356 1 123 -357 1 125 -358 1 130 -359 1 131 -360 1 133 -361 1 135 -362 1 137 -363 1 139 -364 1 141 -365 1 143 -366 1 146 -367 1 152 -368 1 158 -369 1 160 -370 1 162 -371 1 164 -372 1 165 -373 1 168 -374 1 170 -375 1 172 -376 1 173 -377 1 175 -378 1 178 -379 1 180 -380 1 182 -381 1 184 -382 1 186 -383 1 188 -384 1 190 -385 1 192 -386 1 194 -387 1 196 -388 1 198 -389 1 200 -390 1 202 -391 1 204 -392 1 206 -393 1 208 -394 1 210 -395 1 212 -396 1 214 -397 1 216 -398 1 218 -399 1 220 -400 1 222 -401 1 225 -402 1 228 -403 1 230 -404 1 232 -405 1 234 -406 1 236 -407 1 237 -408 1 239 -409 1 240 -410 1 242 -411 1 244 -412 1 246 -413 1 252 -414 1 254 -415 1 256 -416 1 262 -417 1 265 -418 1 267 -419 1 270 -420 1 272 -421 1 275 -422 1 276 -423 1 278 -424 1 280 -425 1 282 -426 1 284 -427 1 286 -428 1 292 -429 1 294 -430 1 297 -431 1 298 -432 1 300 -433 1 303 - diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top index a8528540e..b3c77b272 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top @@ -3,10 +3,10 @@ #include "go_atomtypes.itp" #include "go_nbparams.itp" -#include "molecule_0.itp" +#include "molecule.itp" [ system ] Title of the system [ molecules ] -molecule_0 1 +molecule 1 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp deleted file mode 100644 index bfc214c64..000000000 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp +++ /dev/null @@ -1,1669 +0,0 @@ -; This file was generated using the following command: -; /local/lborge01/martinize_stuff/dev_go/devmartinize/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go -go-map ../map.map -water-bias -water-bias-eps E:-.5 C:1.0 H:-1.0 -; martinize with vermouth 0.9.7.dev79 -; The following sequence of secondary structure -; was used for the full system: -; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC - -; Pleas cite the following papers: -; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 - -[ moleculetype ] -molecule_0 1 - -[ atoms ] - 1 Q5 1 LYS BB 1 1 - 2 SC3 1 LYS SC1 2 0.0 - 3 SQ4p 1 LYS SC2 3 1.0 - 4 SP2 2 VAL BB 4 0.0 - 5 SC3 2 VAL SC1 5 0.0 - 6 P2 3 PHE BB 6 0.0 - 7 SC4 3 PHE SC1 7 0.0 - 8 TC5 3 PHE SC2 8 0.0 - 9 TC5 3 PHE SC3 9 0.0 - 10 SP1 4 GLY BB 10 0.0 - 11 P2 5 ARG BB 11 0.0 - 12 SC3 5 ARG SC1 12 0.0 - 13 SQ3p 5 ARG SC2 13 1.0 - 14 P2 6 CYS BB 14 0.0 - 15 TC6 6 CYS SC1 15 0.0 - 16 P2 7 GLU BB 16 0.0 - 17 Q5n 7 GLU SC1 17 -1.0 - 18 P2 8 LEU BB 18 0.0 - 19 SC2 8 LEU SC1 19 0.0 - 20 SP2 9 ALA BB 20 0.0 - 21 TC3 9 ALA SC1 21 0.0 - 22 SP2 10 ALA BB 22 0.0 - 23 TC3 10 ALA SC1 23 0.0 - 24 SP2 11 ALA BB 24 0.0 - 25 TC3 11 ALA SC1 25 0.0 - 26 P2 12 MET BB 26 0.0 - 27 C6 12 MET SC1 27 0.0 - 28 P2 13 LYS BB 28 0.0 - 29 SC3 13 LYS SC1 29 0.0 - 30 SQ4p 13 LYS SC2 30 1.0 - 31 P2 14 ARG BB 31 0.0 - 32 SC3 14 ARG SC1 32 0.0 - 33 SQ3p 14 ARG SC2 33 1.0 - 34 P2 15 HIS BB 34 0.0 - 35 TC4 15 HIS SC1 35 0.0 - 36 TN6d 15 HIS SC2 36 0.0 - 37 TN5a 15 HIS SC3 37 0.0 - 38 SP1 16 GLY BB 38 0.0 - 39 P2 17 LEU BB 39 0.0 - 40 SC2 17 LEU SC1 40 0.0 - 41 P2 18 ASP BB 41 0.0 - 42 SQ5n 18 ASP SC1 42 -1.0 - 43 P2 19 ASN BB 43 0.0 - 44 SP5 19 ASN SC1 44 0.0 - 45 P2 20 TYR BB 45 0.0 - 46 TC4 20 TYR SC1 46 0.0 - 47 TC5 20 TYR SC2 47 0.0 - 48 TC5 20 TYR SC3 48 0.0 - 49 TN6 20 TYR SC4 49 0.0 - 50 P2 21 ARG BB 50 0.0 - 51 SC3 21 ARG SC1 51 0.0 - 52 SQ3p 21 ARG SC2 52 1.0 - 53 SP1 22 GLY BB 53 0.0 - 54 P2 23 TYR BB 54 0.0 - 55 TC4 23 TYR SC1 55 0.0 - 56 TC5 23 TYR SC2 56 0.0 - 57 TC5 23 TYR SC3 57 0.0 - 58 TN6 23 TYR SC4 58 0.0 - 59 P2 24 SER BB 59 0.0 - 60 TP1 24 SER SC1 60 0.0 - 61 P2 25 LEU BB 61 0.0 - 62 SC2 25 LEU SC1 62 0.0 - 63 SP1 26 GLY BB 63 0.0 - 64 P2 27 ASN BB 64 0.0 - 65 SP5 27 ASN SC1 65 0.0 - 66 P2 28 TRP BB 66 0.0 - 67 TC4 28 TRP SC1 67 0.0 36.0 - 68 TN6d 28 TRP SC2 68 0.0 36.0 - 69 TC5 28 TRP SC3 69 0.0 0.0 - 70 TC5 28 TRP SC4 70 0.0 36.0 - 71 TC5 28 TRP SC5 71 0.0 36.0 - 72 SP2 29 VAL BB 72 0.0 - 73 SC3 29 VAL SC1 73 0.0 - 74 P2 30 CYS BB 74 0.0 - 75 TC6 30 CYS SC1 75 0.0 - 76 SP2 31 ALA BB 76 0.0 - 77 TC3 31 ALA SC1 77 0.0 - 78 SP2 32 ALA BB 78 0.0 - 79 TC3 32 ALA SC1 79 0.0 - 80 P2 33 LYS BB 80 0.0 - 81 SC3 33 LYS SC1 81 0.0 - 82 SQ4p 33 LYS SC2 82 1.0 - 83 P2 34 PHE BB 83 0.0 - 84 SC4 34 PHE SC1 84 0.0 - 85 TC5 34 PHE SC2 85 0.0 - 86 TC5 34 PHE SC3 86 0.0 - 87 P2 35 GLU BB 87 0.0 - 88 Q5n 35 GLU SC1 88 -1.0 - 89 P2 36 SER BB 89 0.0 - 90 TP1 36 SER SC1 90 0.0 - 91 P2 37 ASN BB 91 0.0 - 92 SP5 37 ASN SC1 92 0.0 - 93 P2 38 PHE BB 93 0.0 - 94 SC4 38 PHE SC1 94 0.0 - 95 TC5 38 PHE SC2 95 0.0 - 96 TC5 38 PHE SC3 96 0.0 - 97 P2 39 ASN BB 97 0.0 - 98 SP5 39 ASN SC1 98 0.0 - 99 P2 40 THR BB 99 0.0 -100 SP1 40 THR SC1 100 0.0 -101 P2 41 GLN BB 101 0.0 -102 P5 41 GLN SC1 102 0.0 -103 SP2 42 ALA BB 103 0.0 -104 TC3 42 ALA SC1 104 0.0 -105 P2 43 THR BB 105 0.0 -106 SP1 43 THR SC1 106 0.0 -107 P2 44 ASN BB 107 0.0 -108 SP5 44 ASN SC1 108 0.0 -109 P2 45 ARG BB 109 0.0 -110 SC3 45 ARG SC1 110 0.0 -111 SQ3p 45 ARG SC2 111 1.0 -112 P2 46 ASN BB 112 0.0 -113 SP5 46 ASN SC1 113 0.0 -114 P2 47 THR BB 114 0.0 -115 SP1 47 THR SC1 115 0.0 -116 P2 48 ASP BB 116 0.0 -117 SQ5n 48 ASP SC1 117 -1.0 -118 SP1 49 GLY BB 118 0.0 -119 P2 50 SER BB 119 0.0 -120 TP1 50 SER SC1 120 0.0 -121 P2 51 THR BB 121 0.0 -122 SP1 51 THR SC1 122 0.0 -123 P2 52 ASP BB 123 0.0 -124 SQ5n 52 ASP SC1 124 -1.0 -125 P2 53 TYR BB 125 0.0 -126 TC4 53 TYR SC1 126 0.0 -127 TC5 53 TYR SC2 127 0.0 -128 TC5 53 TYR SC3 128 0.0 -129 TN6 53 TYR SC4 129 0.0 -130 SP1 54 GLY BB 130 0.0 -131 P2 55 ILE BB 131 0.0 -132 SC2 55 ILE SC1 132 0.0 -133 P2 56 LEU BB 133 0.0 -134 SC2 56 LEU SC1 134 0.0 -135 P2 57 GLN BB 135 0.0 -136 P5 57 GLN SC1 136 0.0 -137 P2 58 ILE BB 137 0.0 -138 SC2 58 ILE SC1 138 0.0 -139 P2 59 ASN BB 139 0.0 -140 SP5 59 ASN SC1 140 0.0 -141 P2 60 SER BB 141 0.0 -142 TP1 60 SER SC1 142 0.0 -143 P2 61 ARG BB 143 0.0 -144 SC3 61 ARG SC1 144 0.0 -145 SQ3p 61 ARG SC2 145 1.0 -146 P2 62 TRP BB 146 0.0 -147 TC4 62 TRP SC1 147 0.0 36.0 -148 TN6d 62 TRP SC2 148 0.0 36.0 -149 TC5 62 TRP SC3 149 0.0 0.0 -150 TC5 62 TRP SC4 150 0.0 36.0 -151 TC5 62 TRP SC5 151 0.0 36.0 -152 P2 63 TRP BB 152 0.0 -153 TC4 63 TRP SC1 153 0.0 36.0 -154 TN6d 63 TRP SC2 154 0.0 36.0 -155 TC5 63 TRP SC3 155 0.0 0.0 -156 TC5 63 TRP SC4 156 0.0 36.0 -157 TC5 63 TRP SC5 157 0.0 36.0 -158 P2 64 CYS BB 158 0.0 -159 TC6 64 CYS SC1 159 0.0 -160 P2 65 ASN BB 160 0.0 -161 SP5 65 ASN SC1 161 0.0 -162 P2 66 ASP BB 162 0.0 -163 SQ5n 66 ASP SC1 163 -1.0 -164 SP1 67 GLY BB 164 0.0 -165 P2 68 ARG BB 165 0.0 -166 SC3 68 ARG SC1 166 0.0 -167 SQ3p 68 ARG SC2 167 1.0 -168 P2 69 THR BB 168 0.0 -169 SP1 69 THR SC1 169 0.0 -170 SP2a 70 PRO BB 170 0.0 -171 SC3 70 PRO SC1 171 0.0 -172 SP1 71 GLY BB 172 0.0 -173 P2 72 SER BB 173 0.0 -174 TP1 72 SER SC1 174 0.0 -175 P2 73 ARG BB 175 0.0 -176 SC3 73 ARG SC1 176 0.0 -177 SQ3p 73 ARG SC2 177 1.0 -178 P2 74 ASN BB 178 0.0 -179 SP5 74 ASN SC1 179 0.0 -180 P2 75 LEU BB 180 0.0 -181 SC2 75 LEU SC1 181 0.0 -182 P2 76 CYS BB 182 0.0 -183 TC6 76 CYS SC1 183 0.0 -184 P2 77 ASN BB 184 0.0 -185 SP5 77 ASN SC1 185 0.0 -186 P2 78 ILE BB 186 0.0 -187 SC2 78 ILE SC1 187 0.0 -188 SP2a 79 PRO BB 188 0.0 -189 SC3 79 PRO SC1 189 0.0 -190 P2 80 CYS BB 190 0.0 -191 TC6 80 CYS SC1 191 0.0 -192 P2 81 SER BB 192 0.0 -193 TP1 81 SER SC1 193 0.0 -194 SP2 82 ALA BB 194 0.0 -195 TC3 82 ALA SC1 195 0.0 -196 P2 83 LEU BB 196 0.0 -197 SC2 83 LEU SC1 197 0.0 -198 P2 84 LEU BB 198 0.0 -199 SC2 84 LEU SC1 199 0.0 -200 P2 85 SER BB 200 0.0 -201 TP1 85 SER SC1 201 0.0 -202 P2 86 SER BB 202 0.0 -203 TP1 86 SER SC1 203 0.0 -204 P2 87 ASP BB 204 0.0 -205 SQ5n 87 ASP SC1 205 -1.0 -206 P2 88 ILE BB 206 0.0 -207 SC2 88 ILE SC1 207 0.0 -208 P2 89 THR BB 208 0.0 -209 SP1 89 THR SC1 209 0.0 -210 SP2 90 ALA BB 210 0.0 -211 TC3 90 ALA SC1 211 0.0 -212 P2 91 SER BB 212 0.0 -213 TP1 91 SER SC1 213 0.0 -214 SP2 92 VAL BB 214 0.0 -215 SC3 92 VAL SC1 215 0.0 -216 P2 93 ASN BB 216 0.0 -217 SP5 93 ASN SC1 217 0.0 -218 P2 94 CYS BB 218 0.0 -219 TC6 94 CYS SC1 219 0.0 -220 SP2 95 ALA BB 220 0.0 -221 TC3 95 ALA SC1 221 0.0 -222 P2 96 LYS BB 222 0.0 -223 SC3 96 LYS SC1 223 0.0 -224 SQ4p 96 LYS SC2 224 1.0 -225 P2 97 LYS BB 225 0.0 -226 SC3 97 LYS SC1 226 0.0 -227 SQ4p 97 LYS SC2 227 1.0 -228 P2 98 ILE BB 228 0.0 -229 SC2 98 ILE SC1 229 0.0 -230 SP2 99 VAL BB 230 0.0 -231 SC3 99 VAL SC1 231 0.0 -232 P2 100 SER BB 232 0.0 -233 TP1 100 SER SC1 233 0.0 -234 P2 101 ASP BB 234 0.0 -235 SQ5n 101 ASP SC1 235 -1.0 -236 SP1 102 GLY BB 236 0.0 -237 P2 103 ASN BB 237 0.0 -238 SP5 103 ASN SC1 238 0.0 -239 SP1 104 GLY BB 239 0.0 -240 P2 105 MET BB 240 0.0 -241 C6 105 MET SC1 241 0.0 -242 P2 106 ASN BB 242 0.0 -243 SP5 106 ASN SC1 243 0.0 -244 SP2 107 ALA BB 244 0.0 -245 TC3 107 ALA SC1 245 0.0 -246 P2 108 TRP BB 246 0.0 -247 TC4 108 TRP SC1 247 0.0 36.0 -248 TN6d 108 TRP SC2 248 0.0 36.0 -249 TC5 108 TRP SC3 249 0.0 0.0 -250 TC5 108 TRP SC4 250 0.0 36.0 -251 TC5 108 TRP SC5 251 0.0 36.0 -252 SP2 109 VAL BB 252 0.0 -253 SC3 109 VAL SC1 253 0.0 -254 SP2 110 ALA BB 254 0.0 -255 TC3 110 ALA SC1 255 0.0 -256 P2 111 TRP BB 256 0.0 -257 TC4 111 TRP SC1 257 0.0 36.0 -258 TN6d 111 TRP SC2 258 0.0 36.0 -259 TC5 111 TRP SC3 259 0.0 0.0 -260 TC5 111 TRP SC4 260 0.0 36.0 -261 TC5 111 TRP SC5 261 0.0 36.0 -262 P2 112 ARG BB 262 0.0 -263 SC3 112 ARG SC1 263 0.0 -264 SQ3p 112 ARG SC2 264 1.0 -265 P2 113 ASN BB 265 0.0 -266 SP5 113 ASN SC1 266 0.0 -267 P2 114 ARG BB 267 0.0 -268 SC3 114 ARG SC1 268 0.0 -269 SQ3p 114 ARG SC2 269 1.0 -270 P2 115 CYS BB 270 0.0 -271 TC6 115 CYS SC1 271 0.0 -272 P2 116 LYS BB 272 0.0 -273 SC3 116 LYS SC1 273 0.0 -274 SQ4p 116 LYS SC2 274 1.0 -275 SP1 117 GLY BB 275 0.0 -276 P2 118 THR BB 276 0.0 -277 SP1 118 THR SC1 277 0.0 -278 P2 119 ASP BB 278 0.0 -279 SQ5n 119 ASP SC1 279 -1.0 -280 SP2 120 VAL BB 280 0.0 -281 SC3 120 VAL SC1 281 0.0 -282 P2 121 GLN BB 282 0.0 -283 P5 121 GLN SC1 283 0.0 -284 SP2 122 ALA BB 284 0.0 -285 TC3 122 ALA SC1 285 0.0 -286 P2 123 TRP BB 286 0.0 -287 TC4 123 TRP SC1 287 0.0 36.0 -288 TN6d 123 TRP SC2 288 0.0 36.0 -289 TC5 123 TRP SC3 289 0.0 0.0 -290 TC5 123 TRP SC4 290 0.0 36.0 -291 TC5 123 TRP SC5 291 0.0 36.0 -292 P2 124 ILE BB 292 0.0 -293 SC2 124 ILE SC1 293 0.0 -294 P2 125 ARG BB 294 0.0 -295 SC3 125 ARG SC1 295 0.0 -296 SQ3p 125 ARG SC2 296 1.0 -297 SP1 126 GLY BB 297 0.0 -298 P2 127 CYS BB 298 0.0 -299 TC6 127 CYS SC1 299 0.0 -300 P2 128 ARG BB 300 0.0 -301 SC3 128 ARG SC1 301 0.0 -302 SQ3p 128 ARG SC2 302 1.0 -303 Q5 129 LEU BB 303 -1 -304 SC2 129 LEU SC1 304 0.0 -305 molecule_0_1 1 LYS CA 305 0 0.0 -306 molecule_0_2 2 VAL CA 306 0 0.0 -307 molecule_0_3 3 PHE CA 307 0 0.0 -308 molecule_0_4 4 GLY CA 308 0 0.0 -309 molecule_0_5 5 ARG CA 309 0 0.0 -310 molecule_0_6 6 CYS CA 310 0 0.0 -311 molecule_0_7 7 GLU CA 311 0 0.0 -312 molecule_0_8 8 LEU CA 312 0 0.0 -313 molecule_0_9 9 ALA CA 313 0 0.0 -314 molecule_0_10 10 ALA CA 314 0 0.0 -315 molecule_0_11 11 ALA CA 315 0 0.0 -316 molecule_0_12 12 MET CA 316 0 0.0 -317 molecule_0_13 13 LYS CA 317 0 0.0 -318 molecule_0_14 14 ARG CA 318 0 0.0 -319 molecule_0_15 15 HIS CA 319 0 0.0 -320 molecule_0_16 16 GLY CA 320 0 0.0 -321 molecule_0_17 17 LEU CA 321 0 0.0 -322 molecule_0_18 18 ASP CA 322 0 0.0 -323 molecule_0_19 19 ASN CA 323 0 0.0 -324 molecule_0_20 20 TYR CA 324 0 0.0 -325 molecule_0_21 21 ARG CA 325 0 0.0 -326 molecule_0_22 22 GLY CA 326 0 0.0 -327 molecule_0_23 23 TYR CA 327 0 0.0 -328 molecule_0_24 24 SER CA 328 0 0.0 -329 molecule_0_25 25 LEU CA 329 0 0.0 -330 molecule_0_26 26 GLY CA 330 0 0.0 -331 molecule_0_27 27 ASN CA 331 0 0.0 -332 molecule_0_28 28 TRP CA 332 0 0.0 -333 molecule_0_29 29 VAL CA 333 0 0.0 -334 molecule_0_30 30 CYS CA 334 0 0.0 -335 molecule_0_31 31 ALA CA 335 0 0.0 -336 molecule_0_32 32 ALA CA 336 0 0.0 -337 molecule_0_33 33 LYS CA 337 0 0.0 -338 molecule_0_34 34 PHE CA 338 0 0.0 -339 molecule_0_35 35 GLU CA 339 0 0.0 -340 molecule_0_36 36 SER CA 340 0 0.0 -341 molecule_0_37 37 ASN CA 341 0 0.0 -342 molecule_0_38 38 PHE CA 342 0 0.0 -343 molecule_0_39 39 ASN CA 343 0 0.0 -344 molecule_0_40 40 THR CA 344 0 0.0 -345 molecule_0_41 41 GLN CA 345 0 0.0 -346 molecule_0_42 42 ALA CA 346 0 0.0 -347 molecule_0_43 43 THR CA 347 0 0.0 -348 molecule_0_44 44 ASN CA 348 0 0.0 -349 molecule_0_45 45 ARG CA 349 0 0.0 -350 molecule_0_46 46 ASN CA 350 0 0.0 -351 molecule_0_47 47 THR CA 351 0 0.0 -352 molecule_0_48 48 ASP CA 352 0 0.0 -353 molecule_0_49 49 GLY CA 353 0 0.0 -354 molecule_0_50 50 SER CA 354 0 0.0 -355 molecule_0_51 51 THR CA 355 0 0.0 -356 molecule_0_52 52 ASP CA 356 0 0.0 -357 molecule_0_53 53 TYR CA 357 0 0.0 -358 molecule_0_54 54 GLY CA 358 0 0.0 -359 molecule_0_55 55 ILE CA 359 0 0.0 -360 molecule_0_56 56 LEU CA 360 0 0.0 -361 molecule_0_57 57 GLN CA 361 0 0.0 -362 molecule_0_58 58 ILE CA 362 0 0.0 -363 molecule_0_59 59 ASN CA 363 0 0.0 -364 molecule_0_60 60 SER CA 364 0 0.0 -365 molecule_0_61 61 ARG CA 365 0 0.0 -366 molecule_0_62 62 TRP CA 366 0 0.0 -367 molecule_0_63 63 TRP CA 367 0 0.0 -368 molecule_0_64 64 CYS CA 368 0 0.0 -369 molecule_0_65 65 ASN CA 369 0 0.0 -370 molecule_0_66 66 ASP CA 370 0 0.0 -371 molecule_0_67 67 GLY CA 371 0 0.0 -372 molecule_0_68 68 ARG CA 372 0 0.0 -373 molecule_0_69 69 THR CA 373 0 0.0 -374 molecule_0_70 70 PRO CA 374 0 0.0 -375 molecule_0_71 71 GLY CA 375 0 0.0 -376 molecule_0_72 72 SER CA 376 0 0.0 -377 molecule_0_73 73 ARG CA 377 0 0.0 -378 molecule_0_74 74 ASN CA 378 0 0.0 -379 molecule_0_75 75 LEU CA 379 0 0.0 -380 molecule_0_76 76 CYS CA 380 0 0.0 -381 molecule_0_77 77 ASN CA 381 0 0.0 -382 molecule_0_78 78 ILE CA 382 0 0.0 -383 molecule_0_79 79 PRO CA 383 0 0.0 -384 molecule_0_80 80 CYS CA 384 0 0.0 -385 molecule_0_81 81 SER CA 385 0 0.0 -386 molecule_0_82 82 ALA CA 386 0 0.0 -387 molecule_0_83 83 LEU CA 387 0 0.0 -388 molecule_0_84 84 LEU CA 388 0 0.0 -389 molecule_0_85 85 SER CA 389 0 0.0 -390 molecule_0_86 86 SER CA 390 0 0.0 -391 molecule_0_87 87 ASP CA 391 0 0.0 -392 molecule_0_88 88 ILE CA 392 0 0.0 -393 molecule_0_89 89 THR CA 393 0 0.0 -394 molecule_0_90 90 ALA CA 394 0 0.0 -395 molecule_0_91 91 SER CA 395 0 0.0 -396 molecule_0_92 92 VAL CA 396 0 0.0 -397 molecule_0_93 93 ASN CA 397 0 0.0 -398 molecule_0_94 94 CYS CA 398 0 0.0 -399 molecule_0_95 95 ALA CA 399 0 0.0 -400 molecule_0_96 96 LYS CA 400 0 0.0 -401 molecule_0_97 97 LYS CA 401 0 0.0 -402 molecule_0_98 98 ILE CA 402 0 0.0 -403 molecule_0_99 99 VAL CA 403 0 0.0 -404 molecule_0_100 100 SER CA 404 0 0.0 -405 molecule_0_101 101 ASP CA 405 0 0.0 -406 molecule_0_102 102 GLY CA 406 0 0.0 -407 molecule_0_103 103 ASN CA 407 0 0.0 -408 molecule_0_104 104 GLY CA 408 0 0.0 -409 molecule_0_105 105 MET CA 409 0 0.0 -410 molecule_0_106 106 ASN CA 410 0 0.0 -411 molecule_0_107 107 ALA CA 411 0 0.0 -412 molecule_0_108 108 TRP CA 412 0 0.0 -413 molecule_0_109 109 VAL CA 413 0 0.0 -414 molecule_0_110 110 ALA CA 414 0 0.0 -415 molecule_0_111 111 TRP CA 415 0 0.0 -416 molecule_0_112 112 ARG CA 416 0 0.0 -417 molecule_0_113 113 ASN CA 417 0 0.0 -418 molecule_0_114 114 ARG CA 418 0 0.0 -419 molecule_0_115 115 CYS CA 419 0 0.0 -420 molecule_0_116 116 LYS CA 420 0 0.0 -421 molecule_0_117 117 GLY CA 421 0 0.0 -422 molecule_0_118 118 THR CA 422 0 0.0 -423 molecule_0_119 119 ASP CA 423 0 0.0 -424 molecule_0_120 120 VAL CA 424 0 0.0 -425 molecule_0_121 121 GLN CA 425 0 0.0 -426 molecule_0_122 122 ALA CA 426 0 0.0 -427 molecule_0_123 123 TRP CA 427 0 0.0 -428 molecule_0_124 124 ILE CA 428 0 0.0 -429 molecule_0_125 125 ARG CA 429 0 0.0 -430 molecule_0_126 126 GLY CA 430 0 0.0 -431 molecule_0_127 127 CYS CA 431 0 0.0 -432 molecule_0_128 128 ARG CA 432 0 0.0 -433 molecule_0_129 129 LEU CA 433 0 0.0 - -[ bonds ] -; Backbone bonds - 1 4 1 0.350 4000 - 4 6 1 0.350 4000 - 6 10 1 0.350 4000 - 34 38 1 0.350 4000 - 38 39 1 0.350 4000 - 39 41 1 0.350 4000 - 41 43 1 0.350 4000 - 43 45 1 0.350 4000 - 45 50 1 0.350 4000 - 50 53 1 0.350 4000 - 53 54 1 0.350 4000 - 54 59 1 0.350 4000 - 91 93 1 0.350 4000 - 93 97 1 0.350 4000 - 97 99 1 0.350 4000 - 99 101 1 0.350 4000 -101 103 1 0.350 4000 -103 105 1 0.350 4000 -105 107 1 0.350 4000 -107 109 1 0.350 4000 -109 112 1 0.350 4000 -112 114 1 0.350 4000 -114 116 1 0.350 4000 -116 118 1 0.350 4000 -118 119 1 0.350 4000 -119 121 1 0.350 4000 -121 123 1 0.350 4000 -123 125 1 0.350 4000 -125 130 1 0.350 4000 -130 131 1 0.350 4000 -131 133 1 0.350 4000 -133 135 1 0.350 4000 -135 137 1 0.350 4000 -137 139 1 0.350 4000 -139 141 1 0.350 4000 -141 143 1 0.350 4000 -143 146 1 0.350 4000 -146 152 1 0.350 4000 -152 158 1 0.350 4000 -158 160 1 0.350 4000 -160 162 1 0.350 4000 -162 164 1 0.350 4000 -164 165 1 0.350 4000 -165 168 1 0.350 4000 -168 170 1 0.350 4000 -170 172 1 0.350 4000 -172 173 1 0.350 4000 -173 175 1 0.350 4000 -175 178 1 0.350 4000 -178 180 1 0.350 4000 -180 182 1 0.350 4000 -182 184 1 0.350 4000 -184 186 1 0.350 4000 -186 188 1 0.350 4000 -200 202 1 0.350 4000 -202 204 1 0.350 4000 -204 206 1 0.350 4000 -234 236 1 0.350 4000 -236 237 1 0.350 4000 -270 272 1 0.350 4000 -272 275 1 0.350 4000 -275 276 1 0.350 4000 -276 278 1 0.350 4000 -294 297 1 0.350 4000 -297 298 1 0.350 4000 -298 300 1 0.350 4000 -300 303 1 0.350 4000 - -; Side chain bonds - 1 2 1 0.330 5000 - 2 3 1 0.360 5000 - 6 7 1 0.325 7500 - 11 12 1 0.330 5000 - 12 13 1 0.380 5000 - 14 15 1 0.341 7500 - 16 17 1 0.400 5000 - 18 19 1 0.363 7500 - 26 27 1 0.40 2500 - 28 29 1 0.330 5000 - 29 30 1 0.360 5000 - 31 32 1 0.330 5000 - 32 33 1 0.380 5000 - 34 35 1 0.336 7500 - 39 40 1 0.363 7500 - 41 42 1 0.352 7500 - 43 44 1 0.352 5000 - 45 46 1 0.325 5000 - 50 51 1 0.330 5000 - 51 52 1 0.380 5000 - 54 55 1 0.325 5000 - 59 60 1 0.287 7500 - 61 62 1 0.363 7500 - 64 65 1 0.352 5000 - 66 67 1 0.315 5000 - 74 75 1 0.341 7500 - 80 81 1 0.330 5000 - 81 82 1 0.360 5000 - 83 84 1 0.325 7500 - 87 88 1 0.400 5000 - 89 90 1 0.287 7500 - 91 92 1 0.352 5000 - 93 94 1 0.325 7500 - 97 98 1 0.352 5000 -101 102 1 0.400 5000 -107 108 1 0.352 5000 -109 110 1 0.330 5000 -110 111 1 0.380 5000 -112 113 1 0.352 5000 -116 117 1 0.352 7500 -119 120 1 0.287 7500 -123 124 1 0.352 7500 -125 126 1 0.325 5000 -133 134 1 0.363 7500 -135 136 1 0.400 5000 -139 140 1 0.352 5000 -141 142 1 0.287 7500 -143 144 1 0.330 5000 -144 145 1 0.380 5000 -146 147 1 0.315 5000 -152 153 1 0.315 5000 -158 159 1 0.341 7500 -160 161 1 0.352 5000 -162 163 1 0.352 7500 -165 166 1 0.330 5000 -166 167 1 0.380 5000 -170 171 1 0.330 7500 -173 174 1 0.287 7500 -175 176 1 0.330 5000 -176 177 1 0.380 5000 -178 179 1 0.352 5000 -180 181 1 0.363 7500 -182 183 1 0.341 7500 -184 185 1 0.352 5000 -188 189 1 0.330 7500 -190 191 1 0.341 7500 -192 193 1 0.287 7500 -196 197 1 0.363 7500 -198 199 1 0.363 7500 -200 201 1 0.287 7500 -202 203 1 0.287 7500 -204 205 1 0.352 7500 -212 213 1 0.287 7500 -216 217 1 0.352 5000 -218 219 1 0.341 7500 -222 223 1 0.330 5000 -223 224 1 0.360 5000 -225 226 1 0.330 5000 -226 227 1 0.360 5000 -232 233 1 0.287 7500 -234 235 1 0.352 7500 -237 238 1 0.352 5000 -240 241 1 0.40 2500 -242 243 1 0.352 5000 -246 247 1 0.315 5000 -256 257 1 0.315 5000 -262 263 1 0.330 5000 -263 264 1 0.380 5000 -265 266 1 0.352 5000 -267 268 1 0.330 5000 -268 269 1 0.380 5000 -270 271 1 0.341 7500 -272 273 1 0.330 5000 -273 274 1 0.360 5000 -278 279 1 0.352 7500 -282 283 1 0.400 5000 -286 287 1 0.315 5000 -294 295 1 0.330 5000 -295 296 1 0.380 5000 -298 299 1 0.341 7500 -300 301 1 0.330 5000 -301 302 1 0.380 5000 -303 304 1 0.363 7500 - -#ifdef FLEXIBLE -; Side chain bonds - 4 5 1 0.292 1000000 - 7 8 1 0.340 1000000 - 7 9 1 0.340 1000000 - 8 9 1 0.290 1000000 - 20 21 1 0.270 1000000 - 22 23 1 0.270 1000000 - 24 25 1 0.270 1000000 - 35 36 1 0.320 1000000 - 35 37 1 0.300 1000000 - 36 37 1 0.270 1000000 - 46 47 1 0.300 1000000 - 46 48 1 0.300 1000000 - 47 49 1 0.285 1000000 - 48 49 1 0.285 1000000 - 47 48 1 0.300 1000000 - 55 56 1 0.300 1000000 - 55 57 1 0.300 1000000 - 56 58 1 0.285 1000000 - 57 58 1 0.285 1000000 - 56 57 1 0.300 1000000 - 67 68 1 0.335 1000000 - 68 71 1 0.412 1000000 - 70 71 1 0.293 1000000 - 67 70 1 0.404 1000000 - 68 70 1 0.470 1000000 - 72 73 1 0.292 1000000 - 76 77 1 0.270 1000000 - 78 79 1 0.270 1000000 - 84 85 1 0.340 1000000 - 84 86 1 0.340 1000000 - 85 86 1 0.290 1000000 - 94 95 1 0.340 1000000 - 94 96 1 0.340 1000000 - 95 96 1 0.290 1000000 - 99 100 1 0.305 1000000 -103 104 1 0.270 1000000 -105 106 1 0.305 1000000 -114 115 1 0.305 1000000 -121 122 1 0.305 1000000 -126 127 1 0.300 1000000 -126 128 1 0.300 1000000 -127 129 1 0.285 1000000 -128 129 1 0.285 1000000 -127 128 1 0.300 1000000 -131 132 1 0.341 1000000 -137 138 1 0.341 1000000 -147 148 1 0.335 1000000 -148 151 1 0.412 1000000 -150 151 1 0.293 1000000 -147 150 1 0.404 1000000 -148 150 1 0.470 1000000 -153 154 1 0.335 1000000 -154 157 1 0.412 1000000 -156 157 1 0.293 1000000 -153 156 1 0.404 1000000 -154 156 1 0.470 1000000 -168 169 1 0.305 1000000 -186 187 1 0.341 1000000 -194 195 1 0.270 1000000 -206 207 1 0.341 1000000 -208 209 1 0.305 1000000 -210 211 1 0.270 1000000 -214 215 1 0.292 1000000 -220 221 1 0.270 1000000 -228 229 1 0.341 1000000 -230 231 1 0.292 1000000 -244 245 1 0.270 1000000 -247 248 1 0.335 1000000 -248 251 1 0.412 1000000 -250 251 1 0.293 1000000 -247 250 1 0.404 1000000 -248 250 1 0.470 1000000 -252 253 1 0.292 1000000 -254 255 1 0.270 1000000 -257 258 1 0.335 1000000 -258 261 1 0.412 1000000 -260 261 1 0.293 1000000 -257 260 1 0.404 1000000 -258 260 1 0.470 1000000 -276 277 1 0.305 1000000 -280 281 1 0.292 1000000 -284 285 1 0.270 1000000 -287 288 1 0.335 1000000 -288 291 1 0.412 1000000 -290 291 1 0.293 1000000 -287 290 1 0.404 1000000 -288 290 1 0.470 1000000 -292 293 1 0.341 1000000 -#endif - -[ constraints ] -; Backbone bonds - 10 11 1 0.33 - 11 14 1 0.310 - 14 16 1 0.310 - 16 18 1 0.310 - 18 20 1 0.310 - 20 22 1 0.310 - 22 24 1 0.310 - 24 26 1 0.310 - 26 28 1 0.310 - 28 31 1 0.310 - 31 34 1 0.33 - 59 61 1 0.33 - 61 63 1 0.310 - 63 64 1 0.310 - 64 66 1 0.310 - 66 72 1 0.310 - 72 74 1 0.310 - 74 76 1 0.310 - 76 78 1 0.310 - 78 80 1 0.310 - 80 83 1 0.310 - 83 87 1 0.310 - 87 89 1 0.310 - 89 91 1 0.33 -188 190 1 0.33 -190 192 1 0.310 -192 194 1 0.310 -194 196 1 0.310 -196 198 1 0.310 -198 200 1 0.33 -206 208 1 0.33 -208 210 1 0.310 -210 212 1 0.310 -212 214 1 0.310 -214 216 1 0.310 -216 218 1 0.310 -218 220 1 0.310 -220 222 1 0.310 -222 225 1 0.310 -225 228 1 0.310 -228 230 1 0.310 -230 232 1 0.310 -232 234 1 0.33 -237 239 1 0.33 -239 240 1 0.310 -240 242 1 0.310 -242 244 1 0.310 -244 246 1 0.33 -246 252 1 0.33 -252 254 1 0.310 -254 256 1 0.310 -256 262 1 0.310 -262 265 1 0.310 -265 267 1 0.310 -267 270 1 0.33 -278 280 1 0.33 -280 282 1 0.310 -282 284 1 0.310 -284 286 1 0.310 -286 292 1 0.310 -292 294 1 0.33 - -#ifndef FLEXIBLE -; Side chain bonds - 4 5 1 0.292 - 7 8 1 0.340 - 7 9 1 0.340 - 8 9 1 0.290 - 20 21 1 0.270 - 22 23 1 0.270 - 24 25 1 0.270 - 35 36 1 0.320 - 35 37 1 0.300 - 36 37 1 0.270 - 46 47 1 0.300 - 46 48 1 0.300 - 47 49 1 0.285 - 48 49 1 0.285 - 47 48 1 0.300 - 55 56 1 0.300 - 55 57 1 0.300 - 56 58 1 0.285 - 57 58 1 0.285 - 56 57 1 0.300 - 67 68 1 0.335 - 68 71 1 0.412 - 70 71 1 0.293 - 67 70 1 0.404 - 68 70 1 0.470 - 72 73 1 0.292 - 76 77 1 0.270 - 78 79 1 0.270 - 84 85 1 0.340 - 84 86 1 0.340 - 85 86 1 0.290 - 94 95 1 0.340 - 94 96 1 0.340 - 95 96 1 0.290 - 99 100 1 0.305 -103 104 1 0.270 -105 106 1 0.305 -114 115 1 0.305 -121 122 1 0.305 -126 127 1 0.300 -126 128 1 0.300 -127 129 1 0.285 -128 129 1 0.285 -127 128 1 0.300 -131 132 1 0.341 -137 138 1 0.341 -147 148 1 0.335 -148 151 1 0.412 -150 151 1 0.293 -147 150 1 0.404 -148 150 1 0.470 -153 154 1 0.335 -154 157 1 0.412 -156 157 1 0.293 -153 156 1 0.404 -154 156 1 0.470 -168 169 1 0.305 -186 187 1 0.341 -194 195 1 0.270 -206 207 1 0.341 -208 209 1 0.305 -210 211 1 0.270 -214 215 1 0.292 -220 221 1 0.270 -228 229 1 0.341 -230 231 1 0.292 -244 245 1 0.270 -247 248 1 0.335 -248 251 1 0.412 -250 251 1 0.293 -247 250 1 0.404 -248 250 1 0.470 -252 253 1 0.292 -254 255 1 0.270 -257 258 1 0.335 -258 261 1 0.412 -260 261 1 0.293 -257 260 1 0.404 -258 260 1 0.470 -276 277 1 0.305 -280 281 1 0.292 -284 285 1 0.270 -287 288 1 0.335 -288 291 1 0.412 -290 291 1 0.293 -287 290 1 0.404 -288 290 1 0.470 -292 293 1 0.341 -#endif - -[ angles ] -; BBB angles - 6 10 11 10 127 20 - 10 11 14 10 127 20 - 11 14 16 2 96 700 - 14 16 18 2 96 700 - 16 18 20 2 96 700 - 18 20 22 2 96 700 - 20 22 24 2 96 700 - 22 24 26 2 96 700 - 24 26 28 2 96 700 - 26 28 31 2 96 700 - 28 31 34 10 100 20 - 31 34 38 10 100 20 - 54 59 61 10 127 20 - 59 61 63 10 127 20 - 61 63 64 2 96 700 - 63 64 66 2 96 700 - 64 66 72 2 96 700 - 66 72 74 2 96 700 - 72 74 76 2 96 700 - 74 76 78 2 96 700 - 76 78 80 2 96 700 - 78 80 83 2 96 700 - 80 83 87 2 96 700 - 83 87 89 2 96 700 - 87 89 91 10 100 20 - 89 91 93 10 100 20 -186 188 190 10 130 20 -188 190 192 10 134 25 -190 192 194 2 96 700 -192 194 196 2 96 700 -194 196 198 2 96 700 -196 198 200 10 130 20 -198 200 202 10 130 20 -204 206 208 10 127 20 -206 208 210 10 127 20 -208 210 212 2 96 700 -210 212 214 2 96 700 -212 214 216 2 96 700 -214 216 218 2 96 700 -216 218 220 2 96 700 -218 220 222 2 96 700 -220 222 225 2 96 700 -222 225 228 2 96 700 -225 228 230 2 96 700 -228 230 232 2 96 700 -230 232 234 10 100 20 -232 234 236 10 100 20 -236 237 239 10 130 20 -237 239 240 10 130 20 -239 240 242 2 96 700 -240 242 244 2 96 700 -242 244 246 10 130 20 -244 246 252 10 130 20 -246 252 254 10 130 20 -252 254 256 2 96 700 -254 256 262 2 96 700 -256 262 265 2 96 700 -262 265 267 2 96 700 -265 267 270 10 100 20 -267 270 272 10 100 20 -276 278 280 10 127 20 -278 280 282 10 127 20 -280 282 284 2 96 700 -282 284 286 2 96 700 -284 286 292 2 96 700 -286 292 294 10 100 20 -292 294 297 10 100 20 - 1 4 6 10 127 20 - 4 6 10 10 127 20 - 41 43 45 10 100 20 - 43 45 50 10 100 20 - 45 50 53 10 100 20 - 50 53 54 10 100 20 - 53 54 59 10 100 20 - 91 93 97 10 100 20 - 93 97 99 10 100 20 - 97 99 101 10 100 20 -101 103 105 10 100 20 -103 105 107 10 127 20 -105 107 109 10 134 25 -107 109 112 10 127 20 -109 112 114 10 100 20 -118 119 121 10 127 20 -119 121 123 10 127 20 -121 123 125 10 134 25 -123 125 130 10 100 20 -125 130 131 10 100 20 -133 135 137 10 100 20 -135 137 139 10 100 20 -137 139 141 10 100 20 -139 141 143 10 100 20 -152 158 160 10 100 20 -158 160 162 10 127 20 -160 162 164 10 127 20 -184 186 188 10 127 20 -165 168 170 10 127 20 -168 170 172 10 100 20 -170 172 173 10 100 20 -114 116 118 10 100 20 -116 118 119 10 100 20 -162 164 165 10 127 20 -164 165 168 10 127 20 -182 184 186 10 100 20 -200 202 204 10 130 20 -202 204 206 10 127 20 -234 236 237 10 100 20 -272 275 276 10 100 20 -275 276 278 10 100 20 - 34 38 39 10 100 20 - 38 39 41 10 100 20 - 39 41 43 10 100 20 - 99 101 103 10 100 20 -112 114 116 10 100 20 -146 152 158 10 100 20 -172 173 175 10 100 20 -173 175 178 10 127 20 -175 178 180 10 100 20 -178 180 182 10 100 20 -180 182 184 10 100 20 -294 297 298 10 100 20 -297 298 300 10 100 20 -298 300 303 10 127 20 -130 131 133 10 100 20 -131 133 135 10 100 20 -141 143 146 10 100 20 -143 146 152 10 100 20 -270 272 275 10 100 20 - -; BBS angles regular martini - 1 4 5 2 100 25 - 4 6 7 2 100 25 - 10 11 12 2 100 25 - 11 14 15 2 100 25 - 14 16 17 2 100 25 - 16 18 19 2 100 25 - 18 20 21 2 100 25 - 20 22 23 2 100 25 - 22 24 25 2 100 25 - 24 26 27 2 100 25 - 26 28 29 2 100 25 - 28 31 32 2 100 25 - 31 34 35 2 100 25 - 38 39 40 2 100 25 - 39 41 42 2 100 25 - 41 43 44 2 100 25 - 43 45 46 2 100 25 - 45 50 51 2 100 25 - 53 54 55 2 100 25 - 54 59 60 2 100 25 - 59 61 62 2 100 25 - 63 64 65 2 100 25 - 64 66 67 2 100 25 - 66 72 73 2 100 25 - 72 74 75 2 100 25 - 74 76 77 2 100 25 - 76 78 79 2 100 25 - 78 80 81 2 100 25 - 80 83 84 2 100 25 - 83 87 88 2 100 25 - 87 89 90 2 100 25 - 89 91 92 2 100 25 - 91 93 94 2 100 25 - 93 97 98 2 100 25 - 97 99 100 2 100 25 - 99 101 102 2 100 25 -101 103 104 2 100 25 -103 105 106 2 100 25 -105 107 108 2 100 25 -107 109 110 2 100 25 -109 112 113 2 100 25 -112 114 115 2 100 25 -114 116 117 2 100 25 -118 119 120 2 100 25 -119 121 122 2 100 25 -121 123 124 2 100 25 -123 125 126 2 100 25 -130 131 132 2 100 25 -131 133 134 2 100 25 -133 135 136 2 100 25 -135 137 138 2 100 25 -137 139 140 2 100 25 -139 141 142 2 100 25 -141 143 144 2 100 25 -143 146 147 2 100 25 -146 152 153 2 100 25 -152 158 159 2 100 25 -158 160 161 2 100 25 -160 162 163 2 100 25 -164 165 166 2 100 25 -165 168 169 2 100 25 -168 170 171 2 100 25 -172 173 174 2 100 25 -173 175 176 2 100 25 -175 178 179 2 100 25 -178 180 181 2 100 25 -180 182 183 2 100 25 -182 184 185 2 100 25 -184 186 187 2 100 25 -186 188 189 2 100 25 -188 190 191 2 100 25 -190 192 193 2 100 25 -192 194 195 2 100 25 -194 196 197 2 100 25 -196 198 199 2 100 25 -198 200 201 2 100 25 -200 202 203 2 100 25 -202 204 205 2 100 25 -204 206 207 2 100 25 -206 208 209 2 100 25 -208 210 211 2 100 25 -210 212 213 2 100 25 -212 214 215 2 100 25 -214 216 217 2 100 25 -216 218 219 2 100 25 -218 220 221 2 100 25 -220 222 223 2 100 25 -222 225 226 2 100 25 -225 228 229 2 100 25 -228 230 231 2 100 25 -230 232 233 2 100 25 -232 234 235 2 100 25 -236 237 238 2 100 25 -239 240 241 2 100 25 -240 242 243 2 100 25 -242 244 245 2 100 25 -244 246 247 2 100 25 -246 252 253 2 100 25 -252 254 255 2 100 25 -254 256 257 2 100 25 -256 262 263 2 100 25 -262 265 266 2 100 25 -265 267 268 2 100 25 -267 270 271 2 100 25 -270 272 273 2 100 25 -275 276 277 2 100 25 -276 278 279 2 100 25 -278 280 281 2 100 25 -280 282 283 2 100 25 -282 284 285 2 100 25 -284 286 287 2 100 25 -286 292 293 2 100 25 -292 294 295 2 100 25 -297 298 299 2 100 25 -298 300 301 2 100 25 -300 303 304 2 100 25 - -; First SBB regular martini - 2 1 4 2 100 25 - -; Side chain angles - 1 2 3 2 180.000 25.0 - 6 7 8 2 120.000 50.0 - 6 7 9 2 120.000 50.0 - 11 12 13 2 180.000 25.0 - 28 29 30 2 180.000 25.0 - 31 32 33 2 180.000 25.0 - 34 35 36 2 120.000 50.0 - 34 35 37 2 120.000 50.0 - 45 46 47 2 120.000 60.0 - 45 46 48 2 120.000 60.0 - 50 51 52 2 180.000 25.0 - 54 55 56 2 120.000 60.0 - 54 55 57 2 120.000 60.0 - 66 67 68 2 120.000 60.0 - 66 67 70 2 130.000 60.0 - 80 81 82 2 180.000 25.0 - 83 84 85 2 120.000 50.0 - 83 84 86 2 120.000 50.0 - 93 94 95 2 120.000 50.0 - 93 94 96 2 120.000 50.0 -109 110 111 2 180.000 25.0 -125 126 127 2 120.000 60.0 -125 126 128 2 120.000 60.0 -143 144 145 2 180.000 25.0 -146 147 148 2 120.000 60.0 -146 147 150 2 130.000 60.0 -152 153 154 2 120.000 60.0 -152 153 156 2 130.000 60.0 -165 166 167 2 180.000 25.0 -175 176 177 2 180.000 25.0 -222 223 224 2 180.000 25.0 -225 226 227 2 180.000 25.0 -246 247 248 2 120.000 60.0 -246 247 250 2 130.000 60.0 -256 257 258 2 120.000 60.0 -256 257 260 2 130.000 60.0 -262 263 264 2 180.000 25.0 -267 268 269 2 180.000 25.0 -272 273 274 2 180.000 25.0 -286 287 288 2 120.000 60.0 -286 287 290 2 130.000 60.0 -294 295 296 2 180.000 25.0 -300 301 302 2 180.000 25.0 - -[ dihedrals ] - 11 14 16 18 1 -120 400 1 - 14 16 18 20 1 -120 400 1 - 16 18 20 22 1 -120 400 1 - 18 20 22 24 1 -120 400 1 - 20 22 24 26 1 -120 400 1 - 22 24 26 28 1 -120 400 1 - 24 26 28 31 1 -120 400 1 - 61 63 64 66 1 -120 400 1 - 63 64 66 72 1 -120 400 1 - 64 66 72 74 1 -120 400 1 - 66 72 74 76 1 -120 400 1 - 72 74 76 78 1 -120 400 1 - 74 76 78 80 1 -120 400 1 - 76 78 80 83 1 -120 400 1 - 78 80 83 87 1 -120 400 1 - 80 83 87 89 1 -120 400 1 -190 192 194 196 1 -120 400 1 -192 194 196 198 1 -120 400 1 -208 210 212 214 1 -120 400 1 -210 212 214 216 1 -120 400 1 -212 214 216 218 1 -120 400 1 -214 216 218 220 1 -120 400 1 -216 218 220 222 1 -120 400 1 -218 220 222 225 1 -120 400 1 -220 222 225 228 1 -120 400 1 -222 225 228 230 1 -120 400 1 -225 228 230 232 1 -120 400 1 -239 240 242 244 1 -120 400 1 -252 254 256 262 1 -120 400 1 -254 256 262 265 1 -120 400 1 -256 262 265 267 1 -120 400 1 -280 282 284 286 1 -120 400 1 -282 284 286 292 1 -120 400 1 - -[ exclusions ] - 6 7 8 9 - 7 8 9 - 8 9 - 34 35 36 37 - 35 36 37 - 36 37 - 45 46 47 48 49 - 46 47 48 49 - 47 48 49 - 48 49 - 54 55 56 57 58 - 55 56 57 58 - 56 57 58 - 57 58 - 66 67 68 69 70 71 - 67 68 69 70 71 - 68 69 70 71 - 69 70 71 - 70 71 - 83 84 85 86 - 84 85 86 - 85 86 - 93 94 95 96 - 94 95 96 - 95 96 -125 126 127 128 129 -126 127 128 129 -127 128 129 -128 129 -146 147 148 149 150 151 -147 148 149 150 151 -148 149 150 151 -149 150 151 -150 151 -152 153 154 155 156 157 -153 154 155 156 157 -154 155 156 157 -155 156 157 -156 157 -246 247 248 249 250 251 -247 248 249 250 251 -248 249 250 251 -249 250 251 -250 251 -256 257 258 259 260 261 -257 258 259 260 261 -258 259 260 261 -259 260 261 -260 261 -286 287 288 289 290 291 -287 288 289 290 291 -288 289 290 291 -289 290 291 -290 291 - -; Go model exclusion - 16 6 - 18 6 - 18 10 - 20 11 - 22 14 - 24 16 - 26 18 - 28 20 - 31 22 - 34 24 - 38 26 - 39 26 - 41 28 - 45 38 - 54 43 - 59 41 - 59 43 - 61 20 - 61 26 - 61 28 - 61 41 - 64 53 - 64 54 - 66 26 - 66 39 - 66 54 - 66 59 - 72 11 - 72 20 - 72 26 - 72 61 - 74 63 - 76 64 - 78 18 - 78 66 - 80 72 - 83 74 - 87 76 - 89 78 - 91 78 - 91 80 - 93 1 - 93 4 - 93 6 - 93 11 - 93 18 - 93 72 - 93 78 - 93 80 - 97 1 - 97 4 - 99 1 - 99 6 -101 1 -103 89 -107 87 -118 109 -119 109 -119 112 -121 105 -121 107 -121 109 -121 112 -123 105 -123 107 -123 112 -125 103 -125 105 -130 89 -130 99 -130 103 -131 6 -131 18 -131 78 -131 87 -131 89 -131 93 -131 97 -131 99 -133 76 -133 78 -133 87 -135 87 -135 89 -135 103 -135 105 -135 107 -135 123 -135 125 -137 123 -137 125 -139 112 -139 119 -139 121 -139 123 -141 119 -141 121 -141 125 -143 116 -143 119 -152 137 -152 139 -158 125 -158 141 -162 121 -162 141 -165 121 -168 118 -168 119 -168 141 -168 143 -170 143 -173 141 -173 143 -173 158 -175 143 -175 146 -178 146 -178 152 -178 158 -178 160 -180 146 -180 152 -182 152 -186 152 -186 158 -186 160 -186 178 -188 158 -188 160 -190 125 -190 141 -190 158 -190 160 -190 162 -194 186 -196 125 -196 130 -196 137 -196 158 -196 186 -198 99 -198 101 -198 103 -198 105 -198 125 -198 130 -200 99 -200 192 -202 1 -202 6 -202 99 -206 18 -206 24 -206 26 -206 34 -206 99 -206 131 -208 31 -208 34 -210 186 -210 194 -210 196 -212 131 -212 137 -212 196 -214 34 -214 39 -214 206 -216 208 -218 137 -218 152 -218 182 -218 186 -218 196 -218 210 -220 66 -220 133 -220 137 -220 212 -222 34 -222 38 -222 39 -222 45 -222 214 -225 152 -225 182 -225 216 -228 137 -228 152 -228 218 -230 45 -230 50 -230 54 -230 220 -232 45 -232 50 -232 222 -234 225 -239 54 -239 230 -240 54 -240 64 -240 66 -240 76 -240 230 -244 228 -246 66 -246 87 -246 133 -246 135 -246 228 -246 230 -254 83 -254 87 -256 64 -256 76 -256 240 -256 242 -262 242 -262 244 -262 246 -265 252 -267 83 -267 254 -270 74 -270 76 -270 83 -270 254 -270 256 -272 242 -272 256 -272 262 -276 267 -280 59 -280 63 -280 64 -280 74 -280 270 -284 11 -286 11 -286 63 -286 72 -286 74 -286 80 -286 276 -292 11 -292 20 -292 61 -292 63 -292 72 -294 11 -294 282 -298 11 -298 14 -303 20 -303 22 -303 28 -303 292 - -[ dihedrals ] - 49 47 48 46 2 180.0 50.0 - 58 56 57 55 2 180.0 50.0 - 71 70 68 67 2 180.0 100.0 -129 127 128 126 2 180.0 50.0 -151 150 148 147 2 180.0 100.0 -157 156 154 153 2 180.0 100.0 -251 250 248 247 2 180.0 100.0 -261 260 258 257 2 180.0 100.0 -291 290 288 287 2 180.0 100.0 - -[ virtual_sitesn ] - 69 2 71 70 68 67 -149 2 151 150 148 147 -155 2 157 156 154 153 -249 2 251 250 248 247 -259 2 261 260 258 257 -289 2 291 290 288 287 - -; Virtual go site -305 1 1 -306 1 4 -307 1 6 -308 1 10 -309 1 11 -310 1 14 -311 1 16 -312 1 18 -313 1 20 -314 1 22 -315 1 24 -316 1 26 -317 1 28 -318 1 31 -319 1 34 -320 1 38 -321 1 39 -322 1 41 -323 1 43 -324 1 45 -325 1 50 -326 1 53 -327 1 54 -328 1 59 -329 1 61 -330 1 63 -331 1 64 -332 1 66 -333 1 72 -334 1 74 -335 1 76 -336 1 78 -337 1 80 -338 1 83 -339 1 87 -340 1 89 -341 1 91 -342 1 93 -343 1 97 -344 1 99 -345 1 101 -346 1 103 -347 1 105 -348 1 107 -349 1 109 -350 1 112 -351 1 114 -352 1 116 -353 1 118 -354 1 119 -355 1 121 -356 1 123 -357 1 125 -358 1 130 -359 1 131 -360 1 133 -361 1 135 -362 1 137 -363 1 139 -364 1 141 -365 1 143 -366 1 146 -367 1 152 -368 1 158 -369 1 160 -370 1 162 -371 1 164 -372 1 165 -373 1 168 -374 1 170 -375 1 172 -376 1 173 -377 1 175 -378 1 178 -379 1 180 -380 1 182 -381 1 184 -382 1 186 -383 1 188 -384 1 190 -385 1 192 -386 1 194 -387 1 196 -388 1 198 -389 1 200 -390 1 202 -391 1 204 -392 1 206 -393 1 208 -394 1 210 -395 1 212 -396 1 214 -397 1 216 -398 1 218 -399 1 220 -400 1 222 -401 1 225 -402 1 228 -403 1 230 -404 1 232 -405 1 234 -406 1 236 -407 1 237 -408 1 239 -409 1 240 -410 1 242 -411 1 244 -412 1 246 -413 1 252 -414 1 254 -415 1 256 -416 1 262 -417 1 265 -418 1 267 -419 1 270 -420 1 272 -421 1 275 -422 1 276 -423 1 278 -424 1 280 -425 1 282 -426 1 284 -427 1 286 -428 1 292 -429 1 294 -430 1 297 -431 1 298 -432 1 300 -433 1 303 - diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top index a8528540e..b3c77b272 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top @@ -3,10 +3,10 @@ #include "go_atomtypes.itp" #include "go_nbparams.itp" -#include "molecule_0.itp" +#include "molecule.itp" [ system ] Title of the system [ molecules ] -molecule_0 1 +molecule 1 From 73a1cf4960c1baed8805dddf5be410b64e8a1f38 Mon Sep 17 00:00:00 2001 From: csbrasnett Date: Mon, 28 Oct 2024 13:19:32 +0100 Subject: [PATCH 5/6] add new reference itps --- .../lysozyme_GO/martinize2/molecule.itp | 1670 ++++++++++++++ .../lysozyme_GObias/martinize2/molecule.itp | 2027 +++++++++++++++++ 2 files changed, 3697 insertions(+) create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule.itp diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule.itp new file mode 100644 index 000000000..70fa5fa0b --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule.itp @@ -0,0 +1,1670 @@ +; This file was generated using the following command: +; /coarse/chris/python_packages/vermouth_dev/vermouth-martinize/venv/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go ../map.map -noscfix -cys none +; martinize with vermouth 0.0.1.dev1783 +; The following sequence of secondary structure +; was used for the full system: +; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC + +; Please cite the following papers: +; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 +; Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; 2024; 10.1101/2024.04.15.589479 + +[ moleculetype ] +molecule 1 + +[ atoms ] + 1 Q5 1 LYS BB 1 1 + 2 SC3 1 LYS SC1 2 0.0 + 3 SQ4p 1 LYS SC2 3 1.0 + 4 SP2 2 VAL BB 4 0.0 + 5 SC3 2 VAL SC1 5 0.0 + 6 P2 3 PHE BB 6 0.0 + 7 SC4 3 PHE SC1 7 0.0 + 8 TC5 3 PHE SC2 8 0.0 + 9 TC5 3 PHE SC3 9 0.0 + 10 SP1 4 GLY BB 10 0.0 + 11 P2 5 ARG BB 11 0.0 + 12 SC3 5 ARG SC1 12 0.0 + 13 SQ3p 5 ARG SC2 13 1.0 + 14 P2 6 CYS BB 14 0.0 + 15 TC6 6 CYS SC1 15 0.0 + 16 P2 7 GLU BB 16 0.0 + 17 Q5n 7 GLU SC1 17 -1.0 + 18 P2 8 LEU BB 18 0.0 + 19 SC2 8 LEU SC1 19 0.0 + 20 SP2 9 ALA BB 20 0.0 + 21 TC3 9 ALA SC1 21 0.0 + 22 SP2 10 ALA BB 22 0.0 + 23 TC3 10 ALA SC1 23 0.0 + 24 SP2 11 ALA BB 24 0.0 + 25 TC3 11 ALA SC1 25 0.0 + 26 P2 12 MET BB 26 0.0 + 27 C6 12 MET SC1 27 0.0 + 28 P2 13 LYS BB 28 0.0 + 29 SC3 13 LYS SC1 29 0.0 + 30 SQ4p 13 LYS SC2 30 1.0 + 31 P2 14 ARG BB 31 0.0 + 32 SC3 14 ARG SC1 32 0.0 + 33 SQ3p 14 ARG SC2 33 1.0 + 34 P2 15 HIS BB 34 0.0 + 35 TC4 15 HIS SC1 35 0.0 + 36 TN6d 15 HIS SC2 36 0.0 + 37 TN5a 15 HIS SC3 37 0.0 + 38 SP1 16 GLY BB 38 0.0 + 39 P2 17 LEU BB 39 0.0 + 40 SC2 17 LEU SC1 40 0.0 + 41 P2 18 ASP BB 41 0.0 + 42 SQ5n 18 ASP SC1 42 -1.0 + 43 P2 19 ASN BB 43 0.0 + 44 SP5 19 ASN SC1 44 0.0 + 45 P2 20 TYR BB 45 0.0 + 46 TC4 20 TYR SC1 46 0.0 + 47 TC5 20 TYR SC2 47 0.0 + 48 TC5 20 TYR SC3 48 0.0 + 49 TN6 20 TYR SC4 49 0.0 + 50 P2 21 ARG BB 50 0.0 + 51 SC3 21 ARG SC1 51 0.0 + 52 SQ3p 21 ARG SC2 52 1.0 + 53 SP1 22 GLY BB 53 0.0 + 54 P2 23 TYR BB 54 0.0 + 55 TC4 23 TYR SC1 55 0.0 + 56 TC5 23 TYR SC2 56 0.0 + 57 TC5 23 TYR SC3 57 0.0 + 58 TN6 23 TYR SC4 58 0.0 + 59 P2 24 SER BB 59 0.0 + 60 TP1 24 SER SC1 60 0.0 + 61 P2 25 LEU BB 61 0.0 + 62 SC2 25 LEU SC1 62 0.0 + 63 SP1 26 GLY BB 63 0.0 + 64 P2 27 ASN BB 64 0.0 + 65 SP5 27 ASN SC1 65 0.0 + 66 P2 28 TRP BB 66 0.0 + 67 TC4 28 TRP SC1 67 0.0 36.0 + 68 TN6d 28 TRP SC2 68 0.0 36.0 + 69 TC5 28 TRP SC3 69 0.0 0.0 + 70 TC5 28 TRP SC4 70 0.0 36.0 + 71 TC5 28 TRP SC5 71 0.0 36.0 + 72 SP2 29 VAL BB 72 0.0 + 73 SC3 29 VAL SC1 73 0.0 + 74 P2 30 CYS BB 74 0.0 + 75 TC6 30 CYS SC1 75 0.0 + 76 SP2 31 ALA BB 76 0.0 + 77 TC3 31 ALA SC1 77 0.0 + 78 SP2 32 ALA BB 78 0.0 + 79 TC3 32 ALA SC1 79 0.0 + 80 P2 33 LYS BB 80 0.0 + 81 SC3 33 LYS SC1 81 0.0 + 82 SQ4p 33 LYS SC2 82 1.0 + 83 P2 34 PHE BB 83 0.0 + 84 SC4 34 PHE SC1 84 0.0 + 85 TC5 34 PHE SC2 85 0.0 + 86 TC5 34 PHE SC3 86 0.0 + 87 P2 35 GLU BB 87 0.0 + 88 Q5n 35 GLU SC1 88 -1.0 + 89 P2 36 SER BB 89 0.0 + 90 TP1 36 SER SC1 90 0.0 + 91 P2 37 ASN BB 91 0.0 + 92 SP5 37 ASN SC1 92 0.0 + 93 P2 38 PHE BB 93 0.0 + 94 SC4 38 PHE SC1 94 0.0 + 95 TC5 38 PHE SC2 95 0.0 + 96 TC5 38 PHE SC3 96 0.0 + 97 P2 39 ASN BB 97 0.0 + 98 SP5 39 ASN SC1 98 0.0 + 99 P2 40 THR BB 99 0.0 +100 SP1 40 THR SC1 100 0.0 +101 P2 41 GLN BB 101 0.0 +102 P5 41 GLN SC1 102 0.0 +103 SP2 42 ALA BB 103 0.0 +104 TC3 42 ALA SC1 104 0.0 +105 P2 43 THR BB 105 0.0 +106 SP1 43 THR SC1 106 0.0 +107 P2 44 ASN BB 107 0.0 +108 SP5 44 ASN SC1 108 0.0 +109 P2 45 ARG BB 109 0.0 +110 SC3 45 ARG SC1 110 0.0 +111 SQ3p 45 ARG SC2 111 1.0 +112 P2 46 ASN BB 112 0.0 +113 SP5 46 ASN SC1 113 0.0 +114 P2 47 THR BB 114 0.0 +115 SP1 47 THR SC1 115 0.0 +116 P2 48 ASP BB 116 0.0 +117 SQ5n 48 ASP SC1 117 -1.0 +118 SP1 49 GLY BB 118 0.0 +119 P2 50 SER BB 119 0.0 +120 TP1 50 SER SC1 120 0.0 +121 P2 51 THR BB 121 0.0 +122 SP1 51 THR SC1 122 0.0 +123 P2 52 ASP BB 123 0.0 +124 SQ5n 52 ASP SC1 124 -1.0 +125 P2 53 TYR BB 125 0.0 +126 TC4 53 TYR SC1 126 0.0 +127 TC5 53 TYR SC2 127 0.0 +128 TC5 53 TYR SC3 128 0.0 +129 TN6 53 TYR SC4 129 0.0 +130 SP1 54 GLY BB 130 0.0 +131 P2 55 ILE BB 131 0.0 +132 SC2 55 ILE SC1 132 0.0 +133 P2 56 LEU BB 133 0.0 +134 SC2 56 LEU SC1 134 0.0 +135 P2 57 GLN BB 135 0.0 +136 P5 57 GLN SC1 136 0.0 +137 P2 58 ILE BB 137 0.0 +138 SC2 58 ILE SC1 138 0.0 +139 P2 59 ASN BB 139 0.0 +140 SP5 59 ASN SC1 140 0.0 +141 P2 60 SER BB 141 0.0 +142 TP1 60 SER SC1 142 0.0 +143 P2 61 ARG BB 143 0.0 +144 SC3 61 ARG SC1 144 0.0 +145 SQ3p 61 ARG SC2 145 1.0 +146 P2 62 TRP BB 146 0.0 +147 TC4 62 TRP SC1 147 0.0 36.0 +148 TN6d 62 TRP SC2 148 0.0 36.0 +149 TC5 62 TRP SC3 149 0.0 0.0 +150 TC5 62 TRP SC4 150 0.0 36.0 +151 TC5 62 TRP SC5 151 0.0 36.0 +152 P2 63 TRP BB 152 0.0 +153 TC4 63 TRP SC1 153 0.0 36.0 +154 TN6d 63 TRP SC2 154 0.0 36.0 +155 TC5 63 TRP SC3 155 0.0 0.0 +156 TC5 63 TRP SC4 156 0.0 36.0 +157 TC5 63 TRP SC5 157 0.0 36.0 +158 P2 64 CYS BB 158 0.0 +159 TC6 64 CYS SC1 159 0.0 +160 P2 65 ASN BB 160 0.0 +161 SP5 65 ASN SC1 161 0.0 +162 P2 66 ASP BB 162 0.0 +163 SQ5n 66 ASP SC1 163 -1.0 +164 SP1 67 GLY BB 164 0.0 +165 P2 68 ARG BB 165 0.0 +166 SC3 68 ARG SC1 166 0.0 +167 SQ3p 68 ARG SC2 167 1.0 +168 P2 69 THR BB 168 0.0 +169 SP1 69 THR SC1 169 0.0 +170 SP2a 70 PRO BB 170 0.0 +171 SC3 70 PRO SC1 171 0.0 +172 SP1 71 GLY BB 172 0.0 +173 P2 72 SER BB 173 0.0 +174 TP1 72 SER SC1 174 0.0 +175 P2 73 ARG BB 175 0.0 +176 SC3 73 ARG SC1 176 0.0 +177 SQ3p 73 ARG SC2 177 1.0 +178 P2 74 ASN BB 178 0.0 +179 SP5 74 ASN SC1 179 0.0 +180 P2 75 LEU BB 180 0.0 +181 SC2 75 LEU SC1 181 0.0 +182 P2 76 CYS BB 182 0.0 +183 TC6 76 CYS SC1 183 0.0 +184 P2 77 ASN BB 184 0.0 +185 SP5 77 ASN SC1 185 0.0 +186 P2 78 ILE BB 186 0.0 +187 SC2 78 ILE SC1 187 0.0 +188 SP2a 79 PRO BB 188 0.0 +189 SC3 79 PRO SC1 189 0.0 +190 P2 80 CYS BB 190 0.0 +191 TC6 80 CYS SC1 191 0.0 +192 P2 81 SER BB 192 0.0 +193 TP1 81 SER SC1 193 0.0 +194 SP2 82 ALA BB 194 0.0 +195 TC3 82 ALA SC1 195 0.0 +196 P2 83 LEU BB 196 0.0 +197 SC2 83 LEU SC1 197 0.0 +198 P2 84 LEU BB 198 0.0 +199 SC2 84 LEU SC1 199 0.0 +200 P2 85 SER BB 200 0.0 +201 TP1 85 SER SC1 201 0.0 +202 P2 86 SER BB 202 0.0 +203 TP1 86 SER SC1 203 0.0 +204 P2 87 ASP BB 204 0.0 +205 SQ5n 87 ASP SC1 205 -1.0 +206 P2 88 ILE BB 206 0.0 +207 SC2 88 ILE SC1 207 0.0 +208 P2 89 THR BB 208 0.0 +209 SP1 89 THR SC1 209 0.0 +210 SP2 90 ALA BB 210 0.0 +211 TC3 90 ALA SC1 211 0.0 +212 P2 91 SER BB 212 0.0 +213 TP1 91 SER SC1 213 0.0 +214 SP2 92 VAL BB 214 0.0 +215 SC3 92 VAL SC1 215 0.0 +216 P2 93 ASN BB 216 0.0 +217 SP5 93 ASN SC1 217 0.0 +218 P2 94 CYS BB 218 0.0 +219 TC6 94 CYS SC1 219 0.0 +220 SP2 95 ALA BB 220 0.0 +221 TC3 95 ALA SC1 221 0.0 +222 P2 96 LYS BB 222 0.0 +223 SC3 96 LYS SC1 223 0.0 +224 SQ4p 96 LYS SC2 224 1.0 +225 P2 97 LYS BB 225 0.0 +226 SC3 97 LYS SC1 226 0.0 +227 SQ4p 97 LYS SC2 227 1.0 +228 P2 98 ILE BB 228 0.0 +229 SC2 98 ILE SC1 229 0.0 +230 SP2 99 VAL BB 230 0.0 +231 SC3 99 VAL SC1 231 0.0 +232 P2 100 SER BB 232 0.0 +233 TP1 100 SER SC1 233 0.0 +234 P2 101 ASP BB 234 0.0 +235 SQ5n 101 ASP SC1 235 -1.0 +236 SP1 102 GLY BB 236 0.0 +237 P2 103 ASN BB 237 0.0 +238 SP5 103 ASN SC1 238 0.0 +239 SP1 104 GLY BB 239 0.0 +240 P2 105 MET BB 240 0.0 +241 C6 105 MET SC1 241 0.0 +242 P2 106 ASN BB 242 0.0 +243 SP5 106 ASN SC1 243 0.0 +244 SP2 107 ALA BB 244 0.0 +245 TC3 107 ALA SC1 245 0.0 +246 P2 108 TRP BB 246 0.0 +247 TC4 108 TRP SC1 247 0.0 36.0 +248 TN6d 108 TRP SC2 248 0.0 36.0 +249 TC5 108 TRP SC3 249 0.0 0.0 +250 TC5 108 TRP SC4 250 0.0 36.0 +251 TC5 108 TRP SC5 251 0.0 36.0 +252 SP2 109 VAL BB 252 0.0 +253 SC3 109 VAL SC1 253 0.0 +254 SP2 110 ALA BB 254 0.0 +255 TC3 110 ALA SC1 255 0.0 +256 P2 111 TRP BB 256 0.0 +257 TC4 111 TRP SC1 257 0.0 36.0 +258 TN6d 111 TRP SC2 258 0.0 36.0 +259 TC5 111 TRP SC3 259 0.0 0.0 +260 TC5 111 TRP SC4 260 0.0 36.0 +261 TC5 111 TRP SC5 261 0.0 36.0 +262 P2 112 ARG BB 262 0.0 +263 SC3 112 ARG SC1 263 0.0 +264 SQ3p 112 ARG SC2 264 1.0 +265 P2 113 ASN BB 265 0.0 +266 SP5 113 ASN SC1 266 0.0 +267 P2 114 ARG BB 267 0.0 +268 SC3 114 ARG SC1 268 0.0 +269 SQ3p 114 ARG SC2 269 1.0 +270 P2 115 CYS BB 270 0.0 +271 TC6 115 CYS SC1 271 0.0 +272 P2 116 LYS BB 272 0.0 +273 SC3 116 LYS SC1 273 0.0 +274 SQ4p 116 LYS SC2 274 1.0 +275 SP1 117 GLY BB 275 0.0 +276 P2 118 THR BB 276 0.0 +277 SP1 118 THR SC1 277 0.0 +278 P2 119 ASP BB 278 0.0 +279 SQ5n 119 ASP SC1 279 -1.0 +280 SP2 120 VAL BB 280 0.0 +281 SC3 120 VAL SC1 281 0.0 +282 P2 121 GLN BB 282 0.0 +283 P5 121 GLN SC1 283 0.0 +284 SP2 122 ALA BB 284 0.0 +285 TC3 122 ALA SC1 285 0.0 +286 P2 123 TRP BB 286 0.0 +287 TC4 123 TRP SC1 287 0.0 36.0 +288 TN6d 123 TRP SC2 288 0.0 36.0 +289 TC5 123 TRP SC3 289 0.0 0.0 +290 TC5 123 TRP SC4 290 0.0 36.0 +291 TC5 123 TRP SC5 291 0.0 36.0 +292 P2 124 ILE BB 292 0.0 +293 SC2 124 ILE SC1 293 0.0 +294 P2 125 ARG BB 294 0.0 +295 SC3 125 ARG SC1 295 0.0 +296 SQ3p 125 ARG SC2 296 1.0 +297 SP1 126 GLY BB 297 0.0 +298 P2 127 CYS BB 298 0.0 +299 TC6 127 CYS SC1 299 0.0 +300 P2 128 ARG BB 300 0.0 +301 SC3 128 ARG SC1 301 0.0 +302 SQ3p 128 ARG SC2 302 1.0 +303 Q5 129 LEU BB 303 -1 +304 SC2 129 LEU SC1 304 0.0 +305 molecule_1 1 LYS CA 305 0 0.0 +306 molecule_2 2 VAL CA 306 0 0.0 +307 molecule_3 3 PHE CA 307 0 0.0 +308 molecule_4 4 GLY CA 308 0 0.0 +309 molecule_5 5 ARG CA 309 0 0.0 +310 molecule_6 6 CYS CA 310 0 0.0 +311 molecule_7 7 GLU CA 311 0 0.0 +312 molecule_8 8 LEU CA 312 0 0.0 +313 molecule_9 9 ALA CA 313 0 0.0 +314 molecule_10 10 ALA CA 314 0 0.0 +315 molecule_11 11 ALA CA 315 0 0.0 +316 molecule_12 12 MET CA 316 0 0.0 +317 molecule_13 13 LYS CA 317 0 0.0 +318 molecule_14 14 ARG CA 318 0 0.0 +319 molecule_15 15 HIS CA 319 0 0.0 +320 molecule_16 16 GLY CA 320 0 0.0 +321 molecule_17 17 LEU CA 321 0 0.0 +322 molecule_18 18 ASP CA 322 0 0.0 +323 molecule_19 19 ASN CA 323 0 0.0 +324 molecule_20 20 TYR CA 324 0 0.0 +325 molecule_21 21 ARG CA 325 0 0.0 +326 molecule_22 22 GLY CA 326 0 0.0 +327 molecule_23 23 TYR CA 327 0 0.0 +328 molecule_24 24 SER CA 328 0 0.0 +329 molecule_25 25 LEU CA 329 0 0.0 +330 molecule_26 26 GLY CA 330 0 0.0 +331 molecule_27 27 ASN CA 331 0 0.0 +332 molecule_28 28 TRP CA 332 0 0.0 +333 molecule_29 29 VAL CA 333 0 0.0 +334 molecule_30 30 CYS CA 334 0 0.0 +335 molecule_31 31 ALA CA 335 0 0.0 +336 molecule_32 32 ALA CA 336 0 0.0 +337 molecule_33 33 LYS CA 337 0 0.0 +338 molecule_34 34 PHE CA 338 0 0.0 +339 molecule_35 35 GLU CA 339 0 0.0 +340 molecule_36 36 SER CA 340 0 0.0 +341 molecule_37 37 ASN CA 341 0 0.0 +342 molecule_38 38 PHE CA 342 0 0.0 +343 molecule_39 39 ASN CA 343 0 0.0 +344 molecule_40 40 THR CA 344 0 0.0 +345 molecule_41 41 GLN CA 345 0 0.0 +346 molecule_42 42 ALA CA 346 0 0.0 +347 molecule_43 43 THR CA 347 0 0.0 +348 molecule_44 44 ASN CA 348 0 0.0 +349 molecule_45 45 ARG CA 349 0 0.0 +350 molecule_46 46 ASN CA 350 0 0.0 +351 molecule_47 47 THR CA 351 0 0.0 +352 molecule_48 48 ASP CA 352 0 0.0 +353 molecule_49 49 GLY CA 353 0 0.0 +354 molecule_50 50 SER CA 354 0 0.0 +355 molecule_51 51 THR CA 355 0 0.0 +356 molecule_52 52 ASP CA 356 0 0.0 +357 molecule_53 53 TYR CA 357 0 0.0 +358 molecule_54 54 GLY CA 358 0 0.0 +359 molecule_55 55 ILE CA 359 0 0.0 +360 molecule_56 56 LEU CA 360 0 0.0 +361 molecule_57 57 GLN CA 361 0 0.0 +362 molecule_58 58 ILE CA 362 0 0.0 +363 molecule_59 59 ASN CA 363 0 0.0 +364 molecule_60 60 SER CA 364 0 0.0 +365 molecule_61 61 ARG CA 365 0 0.0 +366 molecule_62 62 TRP CA 366 0 0.0 +367 molecule_63 63 TRP CA 367 0 0.0 +368 molecule_64 64 CYS CA 368 0 0.0 +369 molecule_65 65 ASN CA 369 0 0.0 +370 molecule_66 66 ASP CA 370 0 0.0 +371 molecule_67 67 GLY CA 371 0 0.0 +372 molecule_68 68 ARG CA 372 0 0.0 +373 molecule_69 69 THR CA 373 0 0.0 +374 molecule_70 70 PRO CA 374 0 0.0 +375 molecule_71 71 GLY CA 375 0 0.0 +376 molecule_72 72 SER CA 376 0 0.0 +377 molecule_73 73 ARG CA 377 0 0.0 +378 molecule_74 74 ASN CA 378 0 0.0 +379 molecule_75 75 LEU CA 379 0 0.0 +380 molecule_76 76 CYS CA 380 0 0.0 +381 molecule_77 77 ASN CA 381 0 0.0 +382 molecule_78 78 ILE CA 382 0 0.0 +383 molecule_79 79 PRO CA 383 0 0.0 +384 molecule_80 80 CYS CA 384 0 0.0 +385 molecule_81 81 SER CA 385 0 0.0 +386 molecule_82 82 ALA CA 386 0 0.0 +387 molecule_83 83 LEU CA 387 0 0.0 +388 molecule_84 84 LEU CA 388 0 0.0 +389 molecule_85 85 SER CA 389 0 0.0 +390 molecule_86 86 SER CA 390 0 0.0 +391 molecule_87 87 ASP CA 391 0 0.0 +392 molecule_88 88 ILE CA 392 0 0.0 +393 molecule_89 89 THR CA 393 0 0.0 +394 molecule_90 90 ALA CA 394 0 0.0 +395 molecule_91 91 SER CA 395 0 0.0 +396 molecule_92 92 VAL CA 396 0 0.0 +397 molecule_93 93 ASN CA 397 0 0.0 +398 molecule_94 94 CYS CA 398 0 0.0 +399 molecule_95 95 ALA CA 399 0 0.0 +400 molecule_96 96 LYS CA 400 0 0.0 +401 molecule_97 97 LYS CA 401 0 0.0 +402 molecule_98 98 ILE CA 402 0 0.0 +403 molecule_99 99 VAL CA 403 0 0.0 +404 molecule_100 100 SER CA 404 0 0.0 +405 molecule_101 101 ASP CA 405 0 0.0 +406 molecule_102 102 GLY CA 406 0 0.0 +407 molecule_103 103 ASN CA 407 0 0.0 +408 molecule_104 104 GLY CA 408 0 0.0 +409 molecule_105 105 MET CA 409 0 0.0 +410 molecule_106 106 ASN CA 410 0 0.0 +411 molecule_107 107 ALA CA 411 0 0.0 +412 molecule_108 108 TRP CA 412 0 0.0 +413 molecule_109 109 VAL CA 413 0 0.0 +414 molecule_110 110 ALA CA 414 0 0.0 +415 molecule_111 111 TRP CA 415 0 0.0 +416 molecule_112 112 ARG CA 416 0 0.0 +417 molecule_113 113 ASN CA 417 0 0.0 +418 molecule_114 114 ARG CA 418 0 0.0 +419 molecule_115 115 CYS CA 419 0 0.0 +420 molecule_116 116 LYS CA 420 0 0.0 +421 molecule_117 117 GLY CA 421 0 0.0 +422 molecule_118 118 THR CA 422 0 0.0 +423 molecule_119 119 ASP CA 423 0 0.0 +424 molecule_120 120 VAL CA 424 0 0.0 +425 molecule_121 121 GLN CA 425 0 0.0 +426 molecule_122 122 ALA CA 426 0 0.0 +427 molecule_123 123 TRP CA 427 0 0.0 +428 molecule_124 124 ILE CA 428 0 0.0 +429 molecule_125 125 ARG CA 429 0 0.0 +430 molecule_126 126 GLY CA 430 0 0.0 +431 molecule_127 127 CYS CA 431 0 0.0 +432 molecule_128 128 ARG CA 432 0 0.0 +433 molecule_129 129 LEU CA 433 0 0.0 + +[ bonds ] +; Backbone bonds + 1 4 1 0.350 4000 + 4 6 1 0.350 4000 + 6 10 1 0.350 4000 + 34 38 1 0.350 4000 + 38 39 1 0.350 4000 + 39 41 1 0.350 4000 + 41 43 1 0.350 4000 + 43 45 1 0.350 4000 + 45 50 1 0.350 4000 + 50 53 1 0.350 4000 + 53 54 1 0.350 4000 + 54 59 1 0.350 4000 + 91 93 1 0.350 4000 + 93 97 1 0.350 4000 + 97 99 1 0.350 4000 + 99 101 1 0.350 4000 +101 103 1 0.350 4000 +103 105 1 0.350 4000 +105 107 1 0.350 4000 +107 109 1 0.350 4000 +109 112 1 0.350 4000 +112 114 1 0.350 4000 +114 116 1 0.350 4000 +116 118 1 0.350 4000 +118 119 1 0.350 4000 +119 121 1 0.350 4000 +121 123 1 0.350 4000 +123 125 1 0.350 4000 +125 130 1 0.350 4000 +130 131 1 0.350 4000 +131 133 1 0.350 4000 +133 135 1 0.350 4000 +135 137 1 0.350 4000 +137 139 1 0.350 4000 +139 141 1 0.350 4000 +141 143 1 0.350 4000 +143 146 1 0.350 4000 +146 152 1 0.350 4000 +152 158 1 0.350 4000 +158 160 1 0.350 4000 +160 162 1 0.350 4000 +162 164 1 0.350 4000 +164 165 1 0.350 4000 +165 168 1 0.350 4000 +168 170 1 0.350 4000 +170 172 1 0.350 4000 +172 173 1 0.350 4000 +173 175 1 0.350 4000 +175 178 1 0.350 4000 +178 180 1 0.350 4000 +180 182 1 0.350 4000 +182 184 1 0.350 4000 +184 186 1 0.350 4000 +186 188 1 0.350 4000 +200 202 1 0.350 4000 +202 204 1 0.350 4000 +204 206 1 0.350 4000 +234 236 1 0.350 4000 +236 237 1 0.350 4000 +270 272 1 0.350 4000 +272 275 1 0.350 4000 +275 276 1 0.350 4000 +276 278 1 0.350 4000 +294 297 1 0.350 4000 +297 298 1 0.350 4000 +298 300 1 0.350 4000 +300 303 1 0.350 4000 + +; Side chain bonds + 1 2 1 0.330 5000 + 2 3 1 0.360 5000 + 6 7 1 0.325 7500 + 11 12 1 0.330 5000 + 12 13 1 0.380 5000 + 14 15 1 0.341 7500 + 16 17 1 0.400 5000 + 18 19 1 0.363 7500 + 26 27 1 0.40 2500 + 28 29 1 0.330 5000 + 29 30 1 0.360 5000 + 31 32 1 0.330 5000 + 32 33 1 0.380 5000 + 34 35 1 0.336 7500 + 39 40 1 0.363 7500 + 41 42 1 0.352 7500 + 43 44 1 0.352 5000 + 45 46 1 0.325 5000 + 50 51 1 0.330 5000 + 51 52 1 0.380 5000 + 54 55 1 0.325 5000 + 59 60 1 0.287 7500 + 61 62 1 0.363 7500 + 64 65 1 0.352 5000 + 66 67 1 0.315 5000 + 74 75 1 0.341 7500 + 80 81 1 0.330 5000 + 81 82 1 0.360 5000 + 83 84 1 0.325 7500 + 87 88 1 0.400 5000 + 89 90 1 0.287 7500 + 91 92 1 0.352 5000 + 93 94 1 0.325 7500 + 97 98 1 0.352 5000 +101 102 1 0.400 5000 +107 108 1 0.352 5000 +109 110 1 0.330 5000 +110 111 1 0.380 5000 +112 113 1 0.352 5000 +116 117 1 0.352 7500 +119 120 1 0.287 7500 +123 124 1 0.352 7500 +125 126 1 0.325 5000 +133 134 1 0.363 7500 +135 136 1 0.400 5000 +139 140 1 0.352 5000 +141 142 1 0.287 7500 +143 144 1 0.330 5000 +144 145 1 0.380 5000 +146 147 1 0.315 5000 +152 153 1 0.315 5000 +158 159 1 0.341 7500 +160 161 1 0.352 5000 +162 163 1 0.352 7500 +165 166 1 0.330 5000 +166 167 1 0.380 5000 +170 171 1 0.330 7500 +173 174 1 0.287 7500 +175 176 1 0.330 5000 +176 177 1 0.380 5000 +178 179 1 0.352 5000 +180 181 1 0.363 7500 +182 183 1 0.341 7500 +184 185 1 0.352 5000 +188 189 1 0.330 7500 +190 191 1 0.341 7500 +192 193 1 0.287 7500 +196 197 1 0.363 7500 +198 199 1 0.363 7500 +200 201 1 0.287 7500 +202 203 1 0.287 7500 +204 205 1 0.352 7500 +212 213 1 0.287 7500 +216 217 1 0.352 5000 +218 219 1 0.341 7500 +222 223 1 0.330 5000 +223 224 1 0.360 5000 +225 226 1 0.330 5000 +226 227 1 0.360 5000 +232 233 1 0.287 7500 +234 235 1 0.352 7500 +237 238 1 0.352 5000 +240 241 1 0.40 2500 +242 243 1 0.352 5000 +246 247 1 0.315 5000 +256 257 1 0.315 5000 +262 263 1 0.330 5000 +263 264 1 0.380 5000 +265 266 1 0.352 5000 +267 268 1 0.330 5000 +268 269 1 0.380 5000 +270 271 1 0.341 7500 +272 273 1 0.330 5000 +273 274 1 0.360 5000 +278 279 1 0.352 7500 +282 283 1 0.400 5000 +286 287 1 0.315 5000 +294 295 1 0.330 5000 +295 296 1 0.380 5000 +298 299 1 0.341 7500 +300 301 1 0.330 5000 +301 302 1 0.380 5000 +303 304 1 0.363 7500 + +#ifdef FLEXIBLE +; Side chain bonds + 4 5 1 0.292 1000000 + 7 8 1 0.340 1000000 + 7 9 1 0.340 1000000 + 8 9 1 0.290 1000000 + 20 21 1 0.270 1000000 + 22 23 1 0.270 1000000 + 24 25 1 0.270 1000000 + 35 36 1 0.320 1000000 + 35 37 1 0.300 1000000 + 36 37 1 0.270 1000000 + 46 47 1 0.300 1000000 + 46 48 1 0.300 1000000 + 47 49 1 0.285 1000000 + 48 49 1 0.285 1000000 + 47 48 1 0.300 1000000 + 55 56 1 0.300 1000000 + 55 57 1 0.300 1000000 + 56 58 1 0.285 1000000 + 57 58 1 0.285 1000000 + 56 57 1 0.300 1000000 + 67 68 1 0.335 1000000 + 68 71 1 0.412 1000000 + 70 71 1 0.293 1000000 + 67 70 1 0.404 1000000 + 68 70 1 0.470 1000000 + 72 73 1 0.292 1000000 + 76 77 1 0.270 1000000 + 78 79 1 0.270 1000000 + 84 85 1 0.340 1000000 + 84 86 1 0.340 1000000 + 85 86 1 0.290 1000000 + 94 95 1 0.340 1000000 + 94 96 1 0.340 1000000 + 95 96 1 0.290 1000000 + 99 100 1 0.305 1000000 +103 104 1 0.270 1000000 +105 106 1 0.305 1000000 +114 115 1 0.305 1000000 +121 122 1 0.305 1000000 +126 127 1 0.300 1000000 +126 128 1 0.300 1000000 +127 129 1 0.285 1000000 +128 129 1 0.285 1000000 +127 128 1 0.300 1000000 +131 132 1 0.341 1000000 +137 138 1 0.341 1000000 +147 148 1 0.335 1000000 +148 151 1 0.412 1000000 +150 151 1 0.293 1000000 +147 150 1 0.404 1000000 +148 150 1 0.470 1000000 +153 154 1 0.335 1000000 +154 157 1 0.412 1000000 +156 157 1 0.293 1000000 +153 156 1 0.404 1000000 +154 156 1 0.470 1000000 +168 169 1 0.305 1000000 +186 187 1 0.341 1000000 +194 195 1 0.270 1000000 +206 207 1 0.341 1000000 +208 209 1 0.305 1000000 +210 211 1 0.270 1000000 +214 215 1 0.292 1000000 +220 221 1 0.270 1000000 +228 229 1 0.341 1000000 +230 231 1 0.292 1000000 +244 245 1 0.270 1000000 +247 248 1 0.335 1000000 +248 251 1 0.412 1000000 +250 251 1 0.293 1000000 +247 250 1 0.404 1000000 +248 250 1 0.470 1000000 +252 253 1 0.292 1000000 +254 255 1 0.270 1000000 +257 258 1 0.335 1000000 +258 261 1 0.412 1000000 +260 261 1 0.293 1000000 +257 260 1 0.404 1000000 +258 260 1 0.470 1000000 +276 277 1 0.305 1000000 +280 281 1 0.292 1000000 +284 285 1 0.270 1000000 +287 288 1 0.335 1000000 +288 291 1 0.412 1000000 +290 291 1 0.293 1000000 +287 290 1 0.404 1000000 +288 290 1 0.470 1000000 +292 293 1 0.341 1000000 +#endif + +[ constraints ] +; Backbone bonds + 10 11 1 0.33 + 11 14 1 0.310 + 14 16 1 0.310 + 16 18 1 0.310 + 18 20 1 0.310 + 20 22 1 0.310 + 22 24 1 0.310 + 24 26 1 0.310 + 26 28 1 0.310 + 28 31 1 0.310 + 31 34 1 0.33 + 59 61 1 0.33 + 61 63 1 0.310 + 63 64 1 0.310 + 64 66 1 0.310 + 66 72 1 0.310 + 72 74 1 0.310 + 74 76 1 0.310 + 76 78 1 0.310 + 78 80 1 0.310 + 80 83 1 0.310 + 83 87 1 0.310 + 87 89 1 0.310 + 89 91 1 0.33 +188 190 1 0.33 +190 192 1 0.310 +192 194 1 0.310 +194 196 1 0.310 +196 198 1 0.310 +198 200 1 0.33 +206 208 1 0.33 +208 210 1 0.310 +210 212 1 0.310 +212 214 1 0.310 +214 216 1 0.310 +216 218 1 0.310 +218 220 1 0.310 +220 222 1 0.310 +222 225 1 0.310 +225 228 1 0.310 +228 230 1 0.310 +230 232 1 0.310 +232 234 1 0.33 +237 239 1 0.33 +239 240 1 0.310 +240 242 1 0.310 +242 244 1 0.310 +244 246 1 0.33 +246 252 1 0.33 +252 254 1 0.310 +254 256 1 0.310 +256 262 1 0.310 +262 265 1 0.310 +265 267 1 0.310 +267 270 1 0.33 +278 280 1 0.33 +280 282 1 0.310 +282 284 1 0.310 +284 286 1 0.310 +286 292 1 0.310 +292 294 1 0.33 + +#ifndef FLEXIBLE +; Side chain bonds + 4 5 1 0.292 + 7 8 1 0.340 + 7 9 1 0.340 + 8 9 1 0.290 + 20 21 1 0.270 + 22 23 1 0.270 + 24 25 1 0.270 + 35 36 1 0.320 + 35 37 1 0.300 + 36 37 1 0.270 + 46 47 1 0.300 + 46 48 1 0.300 + 47 49 1 0.285 + 48 49 1 0.285 + 47 48 1 0.300 + 55 56 1 0.300 + 55 57 1 0.300 + 56 58 1 0.285 + 57 58 1 0.285 + 56 57 1 0.300 + 67 68 1 0.335 + 68 71 1 0.412 + 70 71 1 0.293 + 67 70 1 0.404 + 68 70 1 0.470 + 72 73 1 0.292 + 76 77 1 0.270 + 78 79 1 0.270 + 84 85 1 0.340 + 84 86 1 0.340 + 85 86 1 0.290 + 94 95 1 0.340 + 94 96 1 0.340 + 95 96 1 0.290 + 99 100 1 0.305 +103 104 1 0.270 +105 106 1 0.305 +114 115 1 0.305 +121 122 1 0.305 +126 127 1 0.300 +126 128 1 0.300 +127 129 1 0.285 +128 129 1 0.285 +127 128 1 0.300 +131 132 1 0.341 +137 138 1 0.341 +147 148 1 0.335 +148 151 1 0.412 +150 151 1 0.293 +147 150 1 0.404 +148 150 1 0.470 +153 154 1 0.335 +154 157 1 0.412 +156 157 1 0.293 +153 156 1 0.404 +154 156 1 0.470 +168 169 1 0.305 +186 187 1 0.341 +194 195 1 0.270 +206 207 1 0.341 +208 209 1 0.305 +210 211 1 0.270 +214 215 1 0.292 +220 221 1 0.270 +228 229 1 0.341 +230 231 1 0.292 +244 245 1 0.270 +247 248 1 0.335 +248 251 1 0.412 +250 251 1 0.293 +247 250 1 0.404 +248 250 1 0.470 +252 253 1 0.292 +254 255 1 0.270 +257 258 1 0.335 +258 261 1 0.412 +260 261 1 0.293 +257 260 1 0.404 +258 260 1 0.470 +276 277 1 0.305 +280 281 1 0.292 +284 285 1 0.270 +287 288 1 0.335 +288 291 1 0.412 +290 291 1 0.293 +287 290 1 0.404 +288 290 1 0.470 +292 293 1 0.341 +#endif + +[ angles ] +; BBB angles + 6 10 11 10 127 20 + 10 11 14 10 127 20 + 11 14 16 2 96 700 + 14 16 18 2 96 700 + 16 18 20 2 96 700 + 18 20 22 2 96 700 + 20 22 24 2 96 700 + 22 24 26 2 96 700 + 24 26 28 2 96 700 + 26 28 31 2 96 700 + 28 31 34 10 100 20 + 31 34 38 10 100 20 + 54 59 61 10 127 20 + 59 61 63 10 127 20 + 61 63 64 2 96 700 + 63 64 66 2 96 700 + 64 66 72 2 96 700 + 66 72 74 2 96 700 + 72 74 76 2 96 700 + 74 76 78 2 96 700 + 76 78 80 2 96 700 + 78 80 83 2 96 700 + 80 83 87 2 96 700 + 83 87 89 2 96 700 + 87 89 91 10 100 20 + 89 91 93 10 100 20 +186 188 190 10 130 20 +188 190 192 10 134 25 +190 192 194 2 96 700 +192 194 196 2 96 700 +194 196 198 2 96 700 +196 198 200 10 130 20 +198 200 202 10 130 20 +204 206 208 10 127 20 +206 208 210 10 127 20 +208 210 212 2 96 700 +210 212 214 2 96 700 +212 214 216 2 96 700 +214 216 218 2 96 700 +216 218 220 2 96 700 +218 220 222 2 96 700 +220 222 225 2 96 700 +222 225 228 2 96 700 +225 228 230 2 96 700 +228 230 232 2 96 700 +230 232 234 10 100 20 +232 234 236 10 100 20 +236 237 239 10 130 20 +237 239 240 10 130 20 +239 240 242 2 96 700 +240 242 244 2 96 700 +242 244 246 10 130 20 +244 246 252 10 130 20 +246 252 254 10 130 20 +252 254 256 2 96 700 +254 256 262 2 96 700 +256 262 265 2 96 700 +262 265 267 2 96 700 +265 267 270 10 100 20 +267 270 272 10 100 20 +276 278 280 10 127 20 +278 280 282 10 127 20 +280 282 284 2 96 700 +282 284 286 2 96 700 +284 286 292 2 96 700 +286 292 294 10 100 20 +292 294 297 10 100 20 + 1 4 6 10 127 20 + 4 6 10 10 127 20 + 41 43 45 10 100 20 + 43 45 50 10 100 20 + 45 50 53 10 100 20 + 50 53 54 10 100 20 + 53 54 59 10 100 20 + 91 93 97 10 100 20 + 93 97 99 10 100 20 + 97 99 101 10 100 20 +101 103 105 10 100 20 +103 105 107 10 127 20 +105 107 109 10 134 25 +107 109 112 10 127 20 +109 112 114 10 100 20 +118 119 121 10 127 20 +119 121 123 10 127 20 +121 123 125 10 134 25 +123 125 130 10 100 20 +125 130 131 10 100 20 +133 135 137 10 100 20 +135 137 139 10 100 20 +137 139 141 10 100 20 +139 141 143 10 100 20 +152 158 160 10 100 20 +158 160 162 10 127 20 +160 162 164 10 127 20 +184 186 188 10 127 20 +165 168 170 10 127 20 +168 170 172 10 100 20 +170 172 173 10 100 20 +114 116 118 10 100 20 +116 118 119 10 100 20 +162 164 165 10 127 20 +164 165 168 10 127 20 +182 184 186 10 100 20 +200 202 204 10 130 20 +202 204 206 10 127 20 +234 236 237 10 100 20 +272 275 276 10 100 20 +275 276 278 10 100 20 + 34 38 39 10 100 20 + 38 39 41 10 100 20 + 39 41 43 10 100 20 + 99 101 103 10 100 20 +112 114 116 10 100 20 +146 152 158 10 100 20 +172 173 175 10 100 20 +173 175 178 10 127 20 +175 178 180 10 100 20 +178 180 182 10 100 20 +180 182 184 10 100 20 +294 297 298 10 100 20 +297 298 300 10 100 20 +298 300 303 10 127 20 +130 131 133 10 100 20 +131 133 135 10 100 20 +141 143 146 10 100 20 +143 146 152 10 100 20 +270 272 275 10 100 20 + +; BBS angles regular martini + 1 4 5 2 100 25 + 4 6 7 2 100 25 + 10 11 12 2 100 25 + 11 14 15 2 100 25 + 14 16 17 2 100 25 + 16 18 19 2 100 25 + 18 20 21 2 100 25 + 20 22 23 2 100 25 + 22 24 25 2 100 25 + 24 26 27 2 100 25 + 26 28 29 2 100 25 + 28 31 32 2 100 25 + 31 34 35 2 100 25 + 38 39 40 2 100 25 + 39 41 42 2 100 25 + 41 43 44 2 100 25 + 43 45 46 2 100 25 + 45 50 51 2 100 25 + 53 54 55 2 100 25 + 54 59 60 2 100 25 + 59 61 62 2 100 25 + 63 64 65 2 100 25 + 64 66 67 2 100 25 + 66 72 73 2 100 25 + 72 74 75 2 100 25 + 74 76 77 2 100 25 + 76 78 79 2 100 25 + 78 80 81 2 100 25 + 80 83 84 2 100 25 + 83 87 88 2 100 25 + 87 89 90 2 100 25 + 89 91 92 2 100 25 + 91 93 94 2 100 25 + 93 97 98 2 100 25 + 97 99 100 2 100 25 + 99 101 102 2 100 25 +101 103 104 2 100 25 +103 105 106 2 100 25 +105 107 108 2 100 25 +107 109 110 2 100 25 +109 112 113 2 100 25 +112 114 115 2 100 25 +114 116 117 2 100 25 +118 119 120 2 100 25 +119 121 122 2 100 25 +121 123 124 2 100 25 +123 125 126 2 100 25 +130 131 132 2 100 25 +131 133 134 2 100 25 +133 135 136 2 100 25 +135 137 138 2 100 25 +137 139 140 2 100 25 +139 141 142 2 100 25 +141 143 144 2 100 25 +143 146 147 2 100 25 +146 152 153 2 100 25 +152 158 159 2 100 25 +158 160 161 2 100 25 +160 162 163 2 100 25 +164 165 166 2 100 25 +165 168 169 2 100 25 +168 170 171 2 100 25 +172 173 174 2 100 25 +173 175 176 2 100 25 +175 178 179 2 100 25 +178 180 181 2 100 25 +180 182 183 2 100 25 +182 184 185 2 100 25 +184 186 187 2 100 25 +186 188 189 2 100 25 +188 190 191 2 100 25 +190 192 193 2 100 25 +192 194 195 2 100 25 +194 196 197 2 100 25 +196 198 199 2 100 25 +198 200 201 2 100 25 +200 202 203 2 100 25 +202 204 205 2 100 25 +204 206 207 2 100 25 +206 208 209 2 100 25 +208 210 211 2 100 25 +210 212 213 2 100 25 +212 214 215 2 100 25 +214 216 217 2 100 25 +216 218 219 2 100 25 +218 220 221 2 100 25 +220 222 223 2 100 25 +222 225 226 2 100 25 +225 228 229 2 100 25 +228 230 231 2 100 25 +230 232 233 2 100 25 +232 234 235 2 100 25 +236 237 238 2 100 25 +239 240 241 2 100 25 +240 242 243 2 100 25 +242 244 245 2 100 25 +244 246 247 2 100 25 +246 252 253 2 100 25 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25.0 +125 126 127 2 120.000 60.0 +125 126 128 2 120.000 60.0 +143 144 145 2 180.000 25.0 +146 147 148 2 120.000 60.0 +146 147 150 2 130.000 60.0 +152 153 154 2 120.000 60.0 +152 153 156 2 130.000 60.0 +165 166 167 2 180.000 25.0 +175 176 177 2 180.000 25.0 +222 223 224 2 180.000 25.0 +225 226 227 2 180.000 25.0 +246 247 248 2 120.000 60.0 +246 247 250 2 130.000 60.0 +256 257 258 2 120.000 60.0 +256 257 260 2 130.000 60.0 +262 263 264 2 180.000 25.0 +267 268 269 2 180.000 25.0 +272 273 274 2 180.000 25.0 +286 287 288 2 120.000 60.0 +286 287 290 2 130.000 60.0 +294 295 296 2 180.000 25.0 +300 301 302 2 180.000 25.0 + +[ dihedrals ] + 11 14 16 18 1 -120 400 1 + 14 16 18 20 1 -120 400 1 + 16 18 20 22 1 -120 400 1 + 18 20 22 24 1 -120 400 1 + 20 22 24 26 1 -120 400 1 + 22 24 26 28 1 -120 400 1 + 24 26 28 31 1 -120 400 1 + 61 63 64 66 1 -120 400 1 + 63 64 66 72 1 -120 400 1 + 64 66 72 74 1 -120 400 1 + 66 72 74 76 1 -120 400 1 + 72 74 76 78 1 -120 400 1 + 74 76 78 80 1 -120 400 1 + 76 78 80 83 1 -120 400 1 + 78 80 83 87 1 -120 400 1 + 80 83 87 89 1 -120 400 1 +190 192 194 196 1 -120 400 1 +192 194 196 198 1 -120 400 1 +208 210 212 214 1 -120 400 1 +210 212 214 216 1 -120 400 1 +212 214 216 218 1 -120 400 1 +214 216 218 220 1 -120 400 1 +216 218 220 222 1 -120 400 1 +218 220 222 225 1 -120 400 1 +220 222 225 228 1 -120 400 1 +222 225 228 230 1 -120 400 1 +225 228 230 232 1 -120 400 1 +239 240 242 244 1 -120 400 1 +252 254 256 262 1 -120 400 1 +254 256 262 265 1 -120 400 1 +256 262 265 267 1 -120 400 1 +280 282 284 286 1 -120 400 1 +282 284 286 292 1 -120 400 1 + +[ exclusions ] + 6 7 8 9 + 7 8 9 + 8 9 + 34 35 36 37 + 35 36 37 + 36 37 + 45 46 47 48 49 + 46 47 48 49 + 47 48 49 + 48 49 + 54 55 56 57 58 + 55 56 57 58 + 56 57 58 + 57 58 + 66 67 68 69 70 71 + 67 68 69 70 71 + 68 69 70 71 + 69 70 71 + 70 71 + 83 84 85 86 + 84 85 86 + 85 86 + 93 94 95 96 + 94 95 96 + 95 96 +125 126 127 128 129 +126 127 128 129 +127 128 129 +128 129 +146 147 148 149 150 151 +147 148 149 150 151 +148 149 150 151 +149 150 151 +150 151 +152 153 154 155 156 157 +153 154 155 156 157 +154 155 156 157 +155 156 157 +156 157 +246 247 248 249 250 251 +247 248 249 250 251 +248 249 250 251 +249 250 251 +250 251 +256 257 258 259 260 261 +257 258 259 260 261 +258 259 260 261 +259 260 261 +260 261 +286 287 288 289 290 291 +287 288 289 290 291 +288 289 290 291 +289 290 291 +290 291 + +; Go model exclusion + 16 6 + 18 6 + 18 10 + 20 11 + 22 14 + 24 16 + 26 18 + 28 20 + 31 22 + 34 24 + 38 26 + 39 26 + 41 28 + 45 38 + 54 43 + 59 41 + 59 43 + 61 20 + 61 26 + 61 28 + 61 41 + 64 53 + 64 54 + 66 26 + 66 39 + 66 54 + 66 59 + 72 11 + 72 20 + 72 26 + 72 61 + 74 63 + 76 64 + 78 18 + 78 66 + 80 72 + 83 74 + 87 76 + 89 78 + 91 78 + 91 80 + 93 1 + 93 4 + 93 6 + 93 11 + 93 18 + 93 72 + 93 78 + 93 80 + 97 1 + 97 4 + 99 1 + 99 6 +101 1 +103 89 +107 87 +118 109 +119 109 +119 112 +121 105 +121 107 +121 109 +121 112 +123 105 +123 107 +123 112 +125 103 +125 105 +130 89 +130 99 +130 103 +131 6 +131 18 +131 78 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137 +228 152 +228 218 +230 45 +230 50 +230 54 +230 220 +232 45 +232 50 +232 222 +234 225 +239 54 +239 230 +240 54 +240 64 +240 66 +240 76 +240 230 +244 228 +246 66 +246 87 +246 133 +246 135 +246 228 +246 230 +254 83 +254 87 +256 64 +256 76 +256 240 +256 242 +262 242 +262 244 +262 246 +265 252 +267 83 +267 254 +270 74 +270 76 +270 83 +270 254 +270 256 +272 242 +272 256 +272 262 +276 267 +280 59 +280 63 +280 64 +280 74 +280 270 +284 11 +286 11 +286 63 +286 72 +286 74 +286 80 +286 276 +292 11 +292 20 +292 61 +292 63 +292 72 +294 11 +294 282 +298 11 +298 14 +303 20 +303 22 +303 28 +303 292 + +[ dihedrals ] + 49 47 48 46 2 180.0 50.0 + 58 56 57 55 2 180.0 50.0 + 71 70 68 67 2 180.0 100.0 +129 127 128 126 2 180.0 50.0 +151 150 148 147 2 180.0 100.0 +157 156 154 153 2 180.0 100.0 +251 250 248 247 2 180.0 100.0 +261 260 258 257 2 180.0 100.0 +291 290 288 287 2 180.0 100.0 + +[ virtual_sitesn ] + 69 2 71 70 68 67 +149 2 151 150 148 147 +155 2 157 156 154 153 +249 2 251 250 248 247 +259 2 261 260 258 257 +289 2 291 290 288 287 + +; Virtual go site +305 1 1 +306 1 4 +307 1 6 +308 1 10 +309 1 11 +310 1 14 +311 1 16 +312 1 18 +313 1 20 +314 1 22 +315 1 24 +316 1 26 +317 1 28 +318 1 31 +319 1 34 +320 1 38 +321 1 39 +322 1 41 +323 1 43 +324 1 45 +325 1 50 +326 1 53 +327 1 54 +328 1 59 +329 1 61 +330 1 63 +331 1 64 +332 1 66 +333 1 72 +334 1 74 +335 1 76 +336 1 78 +337 1 80 +338 1 83 +339 1 87 +340 1 89 +341 1 91 +342 1 93 +343 1 97 +344 1 99 +345 1 101 +346 1 103 +347 1 105 +348 1 107 +349 1 109 +350 1 112 +351 1 114 +352 1 116 +353 1 118 +354 1 119 +355 1 121 +356 1 123 +357 1 125 +358 1 130 +359 1 131 +360 1 133 +361 1 135 +362 1 137 +363 1 139 +364 1 141 +365 1 143 +366 1 146 +367 1 152 +368 1 158 +369 1 160 +370 1 162 +371 1 164 +372 1 165 +373 1 168 +374 1 170 +375 1 172 +376 1 173 +377 1 175 +378 1 178 +379 1 180 +380 1 182 +381 1 184 +382 1 186 +383 1 188 +384 1 190 +385 1 192 +386 1 194 +387 1 196 +388 1 198 +389 1 200 +390 1 202 +391 1 204 +392 1 206 +393 1 208 +394 1 210 +395 1 212 +396 1 214 +397 1 216 +398 1 218 +399 1 220 +400 1 222 +401 1 225 +402 1 228 +403 1 230 +404 1 232 +405 1 234 +406 1 236 +407 1 237 +408 1 239 +409 1 240 +410 1 242 +411 1 244 +412 1 246 +413 1 252 +414 1 254 +415 1 256 +416 1 262 +417 1 265 +418 1 267 +419 1 270 +420 1 272 +421 1 275 +422 1 276 +423 1 278 +424 1 280 +425 1 282 +426 1 284 +427 1 286 +428 1 292 +429 1 294 +430 1 297 +431 1 298 +432 1 300 +433 1 303 + diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule.itp new file mode 100644 index 000000000..4322ae056 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule.itp @@ -0,0 +1,2027 @@ +; This file was generated using the following command: +; /coarse/chris/python_packages/vermouth_dev/vermouth-martinize/venv/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go ../map.map -water-bias -water-bias-eps E:-.5 C:1.0 H:-1.0 +; martinize with vermouth 0.0.1.dev1783 +; The following sequence of secondary structure +; was used for the full system: +; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC + +; Please cite the following papers: +; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 +; Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; 2024; 10.1101/2024.04.15.589479 + +[ moleculetype ] +molecule 1 + +[ atoms ] + 1 Q5 1 LYS BB 1 1 + 2 SC3 1 LYS SC1 2 0.0 + 3 SQ4p 1 LYS SC2 3 1.0 + 4 SP2 2 VAL BB 4 0.0 + 5 SC3 2 VAL SC1 5 0.0 + 6 P2 3 PHE BB 6 0.0 + 7 SC4 3 PHE SC1 7 0.0 + 8 TC5 3 PHE SC2 8 0.0 + 9 TC5 3 PHE SC3 9 0.0 + 10 SP1 4 GLY BB 10 0.0 + 11 P2 5 ARG BB 11 0.0 + 12 SC3 5 ARG SC1 12 0.0 + 13 SQ3p 5 ARG SC2 13 1.0 + 14 P2 6 CYS BB 14 0.0 + 15 TC6 6 CYS SC1 15 0.0 + 16 P2 7 GLU BB 16 0.0 + 17 Q5n 7 GLU SC1 17 -1.0 + 18 P2 8 LEU BB 18 0.0 + 19 SC2 8 LEU SC1 19 0.0 + 20 SP2 9 ALA BB 20 0.0 + 21 TC3 9 ALA SC1 21 0.0 + 22 SP2 10 ALA BB 22 0.0 + 23 TC3 10 ALA SC1 23 0.0 + 24 SP2 11 ALA BB 24 0.0 + 25 TC3 11 ALA SC1 25 0.0 + 26 P2 12 MET BB 26 0.0 + 27 C6 12 MET SC1 27 0.0 + 28 P2 13 LYS BB 28 0.0 + 29 SC3 13 LYS SC1 29 0.0 + 30 SQ4p 13 LYS SC2 30 1.0 + 31 P2 14 ARG BB 31 0.0 + 32 SC3 14 ARG SC1 32 0.0 + 33 SQ3p 14 ARG SC2 33 1.0 + 34 P2 15 HIS BB 34 0.0 + 35 TC4 15 HIS SC1 35 0.0 + 36 TN6d 15 HIS SC2 36 0.0 + 37 TN5a 15 HIS SC3 37 0.0 + 38 SP1 16 GLY BB 38 0.0 + 39 P2 17 LEU BB 39 0.0 + 40 SC2 17 LEU SC1 40 0.0 + 41 P2 18 ASP BB 41 0.0 + 42 SQ5n 18 ASP SC1 42 -1.0 + 43 P2 19 ASN BB 43 0.0 + 44 SP5 19 ASN SC1 44 0.0 + 45 P2 20 TYR BB 45 0.0 + 46 TC4 20 TYR SC1 46 0.0 + 47 TC5 20 TYR SC2 47 0.0 + 48 TC5 20 TYR SC3 48 0.0 + 49 TN6 20 TYR SC4 49 0.0 + 50 P2 21 ARG BB 50 0.0 + 51 SC3 21 ARG SC1 51 0.0 + 52 SQ3p 21 ARG SC2 52 1.0 + 53 SP1 22 GLY BB 53 0.0 + 54 P2 23 TYR BB 54 0.0 + 55 TC4 23 TYR SC1 55 0.0 + 56 TC5 23 TYR SC2 56 0.0 + 57 TC5 23 TYR SC3 57 0.0 + 58 TN6 23 TYR SC4 58 0.0 + 59 P2 24 SER BB 59 0.0 + 60 TP1 24 SER SC1 60 0.0 + 61 P2 25 LEU BB 61 0.0 + 62 SC2 25 LEU SC1 62 0.0 + 63 SP1 26 GLY BB 63 0.0 + 64 P2 27 ASN BB 64 0.0 + 65 SP5 27 ASN SC1 65 0.0 + 66 P2 28 TRP BB 66 0.0 + 67 TC4 28 TRP SC1 67 0.0 36.0 + 68 TN6d 28 TRP SC2 68 0.0 36.0 + 69 TC5 28 TRP SC3 69 0.0 0.0 + 70 TC5 28 TRP SC4 70 0.0 36.0 + 71 TC5 28 TRP SC5 71 0.0 36.0 + 72 SP2 29 VAL BB 72 0.0 + 73 SC3 29 VAL SC1 73 0.0 + 74 P2 30 CYS BB 74 0.0 + 75 TC6 30 CYS SC1 75 0.0 + 76 SP2 31 ALA BB 76 0.0 + 77 TC3 31 ALA SC1 77 0.0 + 78 SP2 32 ALA BB 78 0.0 + 79 TC3 32 ALA SC1 79 0.0 + 80 P2 33 LYS BB 80 0.0 + 81 SC3 33 LYS SC1 81 0.0 + 82 SQ4p 33 LYS SC2 82 1.0 + 83 P2 34 PHE BB 83 0.0 + 84 SC4 34 PHE SC1 84 0.0 + 85 TC5 34 PHE SC2 85 0.0 + 86 TC5 34 PHE SC3 86 0.0 + 87 P2 35 GLU BB 87 0.0 + 88 Q5n 35 GLU SC1 88 -1.0 + 89 P2 36 SER BB 89 0.0 + 90 TP1 36 SER SC1 90 0.0 + 91 P2 37 ASN BB 91 0.0 + 92 SP5 37 ASN SC1 92 0.0 + 93 P2 38 PHE BB 93 0.0 + 94 SC4 38 PHE SC1 94 0.0 + 95 TC5 38 PHE SC2 95 0.0 + 96 TC5 38 PHE SC3 96 0.0 + 97 P2 39 ASN BB 97 0.0 + 98 SP5 39 ASN SC1 98 0.0 + 99 P2 40 THR BB 99 0.0 +100 SP1 40 THR SC1 100 0.0 +101 P2 41 GLN BB 101 0.0 +102 P5 41 GLN SC1 102 0.0 +103 SP2 42 ALA BB 103 0.0 +104 TC3 42 ALA SC1 104 0.0 +105 P2 43 THR BB 105 0.0 +106 SP1 43 THR SC1 106 0.0 +107 P2 44 ASN BB 107 0.0 +108 SP5 44 ASN SC1 108 0.0 +109 P2 45 ARG BB 109 0.0 +110 SC3 45 ARG SC1 110 0.0 +111 SQ3p 45 ARG SC2 111 1.0 +112 P2 46 ASN BB 112 0.0 +113 SP5 46 ASN SC1 113 0.0 +114 P2 47 THR BB 114 0.0 +115 SP1 47 THR SC1 115 0.0 +116 P2 48 ASP BB 116 0.0 +117 SQ5n 48 ASP SC1 117 -1.0 +118 SP1 49 GLY BB 118 0.0 +119 P2 50 SER BB 119 0.0 +120 TP1 50 SER SC1 120 0.0 +121 P2 51 THR BB 121 0.0 +122 SP1 51 THR SC1 122 0.0 +123 P2 52 ASP BB 123 0.0 +124 SQ5n 52 ASP SC1 124 -1.0 +125 P2 53 TYR BB 125 0.0 +126 TC4 53 TYR SC1 126 0.0 +127 TC5 53 TYR SC2 127 0.0 +128 TC5 53 TYR SC3 128 0.0 +129 TN6 53 TYR SC4 129 0.0 +130 SP1 54 GLY BB 130 0.0 +131 P2 55 ILE BB 131 0.0 +132 SC2 55 ILE SC1 132 0.0 +133 P2 56 LEU BB 133 0.0 +134 SC2 56 LEU SC1 134 0.0 +135 P2 57 GLN BB 135 0.0 +136 P5 57 GLN SC1 136 0.0 +137 P2 58 ILE BB 137 0.0 +138 SC2 58 ILE SC1 138 0.0 +139 P2 59 ASN BB 139 0.0 +140 SP5 59 ASN SC1 140 0.0 +141 P2 60 SER BB 141 0.0 +142 TP1 60 SER SC1 142 0.0 +143 P2 61 ARG BB 143 0.0 +144 SC3 61 ARG SC1 144 0.0 +145 SQ3p 61 ARG SC2 145 1.0 +146 P2 62 TRP BB 146 0.0 +147 TC4 62 TRP SC1 147 0.0 36.0 +148 TN6d 62 TRP SC2 148 0.0 36.0 +149 TC5 62 TRP SC3 149 0.0 0.0 +150 TC5 62 TRP SC4 150 0.0 36.0 +151 TC5 62 TRP SC5 151 0.0 36.0 +152 P2 63 TRP BB 152 0.0 +153 TC4 63 TRP SC1 153 0.0 36.0 +154 TN6d 63 TRP SC2 154 0.0 36.0 +155 TC5 63 TRP SC3 155 0.0 0.0 +156 TC5 63 TRP SC4 156 0.0 36.0 +157 TC5 63 TRP SC5 157 0.0 36.0 +158 P2 64 CYS BB 158 0.0 +159 TC6 64 CYS SC1 159 0.0 +160 P2 65 ASN BB 160 0.0 +161 SP5 65 ASN SC1 161 0.0 +162 P2 66 ASP BB 162 0.0 +163 SQ5n 66 ASP SC1 163 -1.0 +164 SP1 67 GLY BB 164 0.0 +165 P2 68 ARG BB 165 0.0 +166 SC3 68 ARG SC1 166 0.0 +167 SQ3p 68 ARG SC2 167 1.0 +168 P2 69 THR BB 168 0.0 +169 SP1 69 THR SC1 169 0.0 +170 SP2a 70 PRO BB 170 0.0 +171 SC3 70 PRO SC1 171 0.0 +172 SP1 71 GLY BB 172 0.0 +173 P2 72 SER BB 173 0.0 +174 TP1 72 SER SC1 174 0.0 +175 P2 73 ARG BB 175 0.0 +176 SC3 73 ARG SC1 176 0.0 +177 SQ3p 73 ARG SC2 177 1.0 +178 P2 74 ASN BB 178 0.0 +179 SP5 74 ASN SC1 179 0.0 +180 P2 75 LEU BB 180 0.0 +181 SC2 75 LEU SC1 181 0.0 +182 P2 76 CYS BB 182 0.0 +183 TC6 76 CYS SC1 183 0.0 +184 P2 77 ASN BB 184 0.0 +185 SP5 77 ASN SC1 185 0.0 +186 P2 78 ILE BB 186 0.0 +187 SC2 78 ILE SC1 187 0.0 +188 SP2a 79 PRO BB 188 0.0 +189 SC3 79 PRO SC1 189 0.0 +190 P2 80 CYS BB 190 0.0 +191 TC6 80 CYS SC1 191 0.0 +192 P2 81 SER BB 192 0.0 +193 TP1 81 SER SC1 193 0.0 +194 SP2 82 ALA BB 194 0.0 +195 TC3 82 ALA SC1 195 0.0 +196 P2 83 LEU BB 196 0.0 +197 SC2 83 LEU SC1 197 0.0 +198 P2 84 LEU BB 198 0.0 +199 SC2 84 LEU SC1 199 0.0 +200 P2 85 SER BB 200 0.0 +201 TP1 85 SER SC1 201 0.0 +202 P2 86 SER BB 202 0.0 +203 TP1 86 SER SC1 203 0.0 +204 P2 87 ASP BB 204 0.0 +205 SQ5n 87 ASP SC1 205 -1.0 +206 P2 88 ILE BB 206 0.0 +207 SC2 88 ILE SC1 207 0.0 +208 P2 89 THR BB 208 0.0 +209 SP1 89 THR SC1 209 0.0 +210 SP2 90 ALA BB 210 0.0 +211 TC3 90 ALA SC1 211 0.0 +212 P2 91 SER BB 212 0.0 +213 TP1 91 SER SC1 213 0.0 +214 SP2 92 VAL BB 214 0.0 +215 SC3 92 VAL SC1 215 0.0 +216 P2 93 ASN BB 216 0.0 +217 SP5 93 ASN SC1 217 0.0 +218 P2 94 CYS BB 218 0.0 +219 TC6 94 CYS SC1 219 0.0 +220 SP2 95 ALA BB 220 0.0 +221 TC3 95 ALA SC1 221 0.0 +222 P2 96 LYS BB 222 0.0 +223 SC3 96 LYS SC1 223 0.0 +224 SQ4p 96 LYS SC2 224 1.0 +225 P2 97 LYS BB 225 0.0 +226 SC3 97 LYS SC1 226 0.0 +227 SQ4p 97 LYS SC2 227 1.0 +228 P2 98 ILE BB 228 0.0 +229 SC2 98 ILE SC1 229 0.0 +230 SP2 99 VAL BB 230 0.0 +231 SC3 99 VAL SC1 231 0.0 +232 P2 100 SER BB 232 0.0 +233 TP1 100 SER SC1 233 0.0 +234 P2 101 ASP BB 234 0.0 +235 SQ5n 101 ASP SC1 235 -1.0 +236 SP1 102 GLY BB 236 0.0 +237 P2 103 ASN BB 237 0.0 +238 SP5 103 ASN SC1 238 0.0 +239 SP1 104 GLY BB 239 0.0 +240 P2 105 MET BB 240 0.0 +241 C6 105 MET SC1 241 0.0 +242 P2 106 ASN BB 242 0.0 +243 SP5 106 ASN SC1 243 0.0 +244 SP2 107 ALA BB 244 0.0 +245 TC3 107 ALA SC1 245 0.0 +246 P2 108 TRP BB 246 0.0 +247 TC4 108 TRP SC1 247 0.0 36.0 +248 TN6d 108 TRP SC2 248 0.0 36.0 +249 TC5 108 TRP SC3 249 0.0 0.0 +250 TC5 108 TRP SC4 250 0.0 36.0 +251 TC5 108 TRP SC5 251 0.0 36.0 +252 SP2 109 VAL BB 252 0.0 +253 SC3 109 VAL SC1 253 0.0 +254 SP2 110 ALA BB 254 0.0 +255 TC3 110 ALA SC1 255 0.0 +256 P2 111 TRP BB 256 0.0 +257 TC4 111 TRP SC1 257 0.0 36.0 +258 TN6d 111 TRP SC2 258 0.0 36.0 +259 TC5 111 TRP SC3 259 0.0 0.0 +260 TC5 111 TRP SC4 260 0.0 36.0 +261 TC5 111 TRP SC5 261 0.0 36.0 +262 P2 112 ARG BB 262 0.0 +263 SC3 112 ARG SC1 263 0.0 +264 SQ3p 112 ARG SC2 264 1.0 +265 P2 113 ASN BB 265 0.0 +266 SP5 113 ASN SC1 266 0.0 +267 P2 114 ARG BB 267 0.0 +268 SC3 114 ARG SC1 268 0.0 +269 SQ3p 114 ARG SC2 269 1.0 +270 P2 115 CYS BB 270 0.0 +271 TC6 115 CYS SC1 271 0.0 +272 P2 116 LYS BB 272 0.0 +273 SC3 116 LYS SC1 273 0.0 +274 SQ4p 116 LYS SC2 274 1.0 +275 SP1 117 GLY BB 275 0.0 +276 P2 118 THR BB 276 0.0 +277 SP1 118 THR SC1 277 0.0 +278 P2 119 ASP BB 278 0.0 +279 SQ5n 119 ASP SC1 279 -1.0 +280 SP2 120 VAL BB 280 0.0 +281 SC3 120 VAL SC1 281 0.0 +282 P2 121 GLN BB 282 0.0 +283 P5 121 GLN SC1 283 0.0 +284 SP2 122 ALA BB 284 0.0 +285 TC3 122 ALA SC1 285 0.0 +286 P2 123 TRP BB 286 0.0 +287 TC4 123 TRP SC1 287 0.0 36.0 +288 TN6d 123 TRP SC2 288 0.0 36.0 +289 TC5 123 TRP SC3 289 0.0 0.0 +290 TC5 123 TRP SC4 290 0.0 36.0 +291 TC5 123 TRP SC5 291 0.0 36.0 +292 P2 124 ILE BB 292 0.0 +293 SC2 124 ILE SC1 293 0.0 +294 P2 125 ARG BB 294 0.0 +295 SC3 125 ARG SC1 295 0.0 +296 SQ3p 125 ARG SC2 296 1.0 +297 SP1 126 GLY BB 297 0.0 +298 P2 127 CYS BB 298 0.0 +299 TC6 127 CYS SC1 299 0.0 +300 P2 128 ARG BB 300 0.0 +301 SC3 128 ARG SC1 301 0.0 +302 SQ3p 128 ARG SC2 302 1.0 +303 Q5 129 LEU BB 303 -1 +304 SC2 129 LEU SC1 304 0.0 +305 molecule_1 1 LYS CA 305 0 0.0 +306 molecule_2 2 VAL CA 306 0 0.0 +307 molecule_3 3 PHE CA 307 0 0.0 +308 molecule_4 4 GLY CA 308 0 0.0 +309 molecule_5 5 ARG CA 309 0 0.0 +310 molecule_6 6 CYS CA 310 0 0.0 +311 molecule_7 7 GLU CA 311 0 0.0 +312 molecule_8 8 LEU CA 312 0 0.0 +313 molecule_9 9 ALA CA 313 0 0.0 +314 molecule_10 10 ALA CA 314 0 0.0 +315 molecule_11 11 ALA CA 315 0 0.0 +316 molecule_12 12 MET CA 316 0 0.0 +317 molecule_13 13 LYS CA 317 0 0.0 +318 molecule_14 14 ARG CA 318 0 0.0 +319 molecule_15 15 HIS CA 319 0 0.0 +320 molecule_16 16 GLY CA 320 0 0.0 +321 molecule_17 17 LEU CA 321 0 0.0 +322 molecule_18 18 ASP CA 322 0 0.0 +323 molecule_19 19 ASN CA 323 0 0.0 +324 molecule_20 20 TYR CA 324 0 0.0 +325 molecule_21 21 ARG CA 325 0 0.0 +326 molecule_22 22 GLY CA 326 0 0.0 +327 molecule_23 23 TYR CA 327 0 0.0 +328 molecule_24 24 SER CA 328 0 0.0 +329 molecule_25 25 LEU CA 329 0 0.0 +330 molecule_26 26 GLY CA 330 0 0.0 +331 molecule_27 27 ASN CA 331 0 0.0 +332 molecule_28 28 TRP CA 332 0 0.0 +333 molecule_29 29 VAL CA 333 0 0.0 +334 molecule_30 30 CYS CA 334 0 0.0 +335 molecule_31 31 ALA CA 335 0 0.0 +336 molecule_32 32 ALA CA 336 0 0.0 +337 molecule_33 33 LYS CA 337 0 0.0 +338 molecule_34 34 PHE CA 338 0 0.0 +339 molecule_35 35 GLU CA 339 0 0.0 +340 molecule_36 36 SER CA 340 0 0.0 +341 molecule_37 37 ASN CA 341 0 0.0 +342 molecule_38 38 PHE CA 342 0 0.0 +343 molecule_39 39 ASN CA 343 0 0.0 +344 molecule_40 40 THR CA 344 0 0.0 +345 molecule_41 41 GLN CA 345 0 0.0 +346 molecule_42 42 ALA CA 346 0 0.0 +347 molecule_43 43 THR CA 347 0 0.0 +348 molecule_44 44 ASN CA 348 0 0.0 +349 molecule_45 45 ARG CA 349 0 0.0 +350 molecule_46 46 ASN CA 350 0 0.0 +351 molecule_47 47 THR CA 351 0 0.0 +352 molecule_48 48 ASP CA 352 0 0.0 +353 molecule_49 49 GLY CA 353 0 0.0 +354 molecule_50 50 SER CA 354 0 0.0 +355 molecule_51 51 THR CA 355 0 0.0 +356 molecule_52 52 ASP CA 356 0 0.0 +357 molecule_53 53 TYR CA 357 0 0.0 +358 molecule_54 54 GLY CA 358 0 0.0 +359 molecule_55 55 ILE CA 359 0 0.0 +360 molecule_56 56 LEU CA 360 0 0.0 +361 molecule_57 57 GLN CA 361 0 0.0 +362 molecule_58 58 ILE CA 362 0 0.0 +363 molecule_59 59 ASN CA 363 0 0.0 +364 molecule_60 60 SER CA 364 0 0.0 +365 molecule_61 61 ARG CA 365 0 0.0 +366 molecule_62 62 TRP CA 366 0 0.0 +367 molecule_63 63 TRP CA 367 0 0.0 +368 molecule_64 64 CYS CA 368 0 0.0 +369 molecule_65 65 ASN CA 369 0 0.0 +370 molecule_66 66 ASP CA 370 0 0.0 +371 molecule_67 67 GLY CA 371 0 0.0 +372 molecule_68 68 ARG CA 372 0 0.0 +373 molecule_69 69 THR CA 373 0 0.0 +374 molecule_70 70 PRO CA 374 0 0.0 +375 molecule_71 71 GLY CA 375 0 0.0 +376 molecule_72 72 SER CA 376 0 0.0 +377 molecule_73 73 ARG CA 377 0 0.0 +378 molecule_74 74 ASN CA 378 0 0.0 +379 molecule_75 75 LEU CA 379 0 0.0 +380 molecule_76 76 CYS CA 380 0 0.0 +381 molecule_77 77 ASN CA 381 0 0.0 +382 molecule_78 78 ILE CA 382 0 0.0 +383 molecule_79 79 PRO CA 383 0 0.0 +384 molecule_80 80 CYS CA 384 0 0.0 +385 molecule_81 81 SER CA 385 0 0.0 +386 molecule_82 82 ALA CA 386 0 0.0 +387 molecule_83 83 LEU CA 387 0 0.0 +388 molecule_84 84 LEU CA 388 0 0.0 +389 molecule_85 85 SER CA 389 0 0.0 +390 molecule_86 86 SER CA 390 0 0.0 +391 molecule_87 87 ASP CA 391 0 0.0 +392 molecule_88 88 ILE CA 392 0 0.0 +393 molecule_89 89 THR CA 393 0 0.0 +394 molecule_90 90 ALA CA 394 0 0.0 +395 molecule_91 91 SER CA 395 0 0.0 +396 molecule_92 92 VAL CA 396 0 0.0 +397 molecule_93 93 ASN CA 397 0 0.0 +398 molecule_94 94 CYS CA 398 0 0.0 +399 molecule_95 95 ALA CA 399 0 0.0 +400 molecule_96 96 LYS CA 400 0 0.0 +401 molecule_97 97 LYS CA 401 0 0.0 +402 molecule_98 98 ILE CA 402 0 0.0 +403 molecule_99 99 VAL CA 403 0 0.0 +404 molecule_100 100 SER CA 404 0 0.0 +405 molecule_101 101 ASP CA 405 0 0.0 +406 molecule_102 102 GLY CA 406 0 0.0 +407 molecule_103 103 ASN CA 407 0 0.0 +408 molecule_104 104 GLY CA 408 0 0.0 +409 molecule_105 105 MET CA 409 0 0.0 +410 molecule_106 106 ASN CA 410 0 0.0 +411 molecule_107 107 ALA CA 411 0 0.0 +412 molecule_108 108 TRP CA 412 0 0.0 +413 molecule_109 109 VAL CA 413 0 0.0 +414 molecule_110 110 ALA CA 414 0 0.0 +415 molecule_111 111 TRP CA 415 0 0.0 +416 molecule_112 112 ARG CA 416 0 0.0 +417 molecule_113 113 ASN CA 417 0 0.0 +418 molecule_114 114 ARG CA 418 0 0.0 +419 molecule_115 115 CYS CA 419 0 0.0 +420 molecule_116 116 LYS CA 420 0 0.0 +421 molecule_117 117 GLY CA 421 0 0.0 +422 molecule_118 118 THR CA 422 0 0.0 +423 molecule_119 119 ASP CA 423 0 0.0 +424 molecule_120 120 VAL CA 424 0 0.0 +425 molecule_121 121 GLN CA 425 0 0.0 +426 molecule_122 122 ALA CA 426 0 0.0 +427 molecule_123 123 TRP CA 427 0 0.0 +428 molecule_124 124 ILE CA 428 0 0.0 +429 molecule_125 125 ARG CA 429 0 0.0 +430 molecule_126 126 GLY CA 430 0 0.0 +431 molecule_127 127 CYS CA 431 0 0.0 +432 molecule_128 128 ARG CA 432 0 0.0 +433 molecule_129 129 LEU CA 433 0 0.0 + +[ bonds ] +; Backbone bonds + 1 4 1 0.350 4000 + 4 6 1 0.350 4000 + 6 10 1 0.350 4000 + 34 38 1 0.350 4000 + 38 39 1 0.350 4000 + 39 41 1 0.350 4000 + 41 43 1 0.350 4000 + 43 45 1 0.350 4000 + 45 50 1 0.350 4000 + 50 53 1 0.350 4000 + 53 54 1 0.350 4000 + 54 59 1 0.350 4000 + 91 93 1 0.350 4000 + 93 97 1 0.350 4000 + 97 99 1 0.350 4000 + 99 101 1 0.350 4000 +101 103 1 0.350 4000 +103 105 1 0.350 4000 +105 107 1 0.350 4000 +107 109 1 0.350 4000 +109 112 1 0.350 4000 +112 114 1 0.350 4000 +114 116 1 0.350 4000 +116 118 1 0.350 4000 +118 119 1 0.350 4000 +119 121 1 0.350 4000 +121 123 1 0.350 4000 +123 125 1 0.350 4000 +125 130 1 0.350 4000 +130 131 1 0.350 4000 +131 133 1 0.350 4000 +133 135 1 0.350 4000 +135 137 1 0.350 4000 +137 139 1 0.350 4000 +139 141 1 0.350 4000 +141 143 1 0.350 4000 +143 146 1 0.350 4000 +146 152 1 0.350 4000 +152 158 1 0.350 4000 +158 160 1 0.350 4000 +160 162 1 0.350 4000 +162 164 1 0.350 4000 +164 165 1 0.350 4000 +165 168 1 0.350 4000 +168 170 1 0.350 4000 +170 172 1 0.350 4000 +172 173 1 0.350 4000 +173 175 1 0.350 4000 +175 178 1 0.350 4000 +178 180 1 0.350 4000 +180 182 1 0.350 4000 +182 184 1 0.350 4000 +184 186 1 0.350 4000 +186 188 1 0.350 4000 +200 202 1 0.350 4000 +202 204 1 0.350 4000 +204 206 1 0.350 4000 +234 236 1 0.350 4000 +236 237 1 0.350 4000 +270 272 1 0.350 4000 +272 275 1 0.350 4000 +275 276 1 0.350 4000 +276 278 1 0.350 4000 +294 297 1 0.350 4000 +297 298 1 0.350 4000 +298 300 1 0.350 4000 +300 303 1 0.350 4000 + +; Side chain bonds + 1 2 1 0.330 5000 + 2 3 1 0.360 5000 + 6 7 1 0.325 7500 + 11 12 1 0.330 5000 + 12 13 1 0.380 5000 + 14 15 1 0.341 7500 + 16 17 1 0.400 5000 + 18 19 1 0.363 7500 + 26 27 1 0.40 2500 + 28 29 1 0.330 5000 + 29 30 1 0.360 5000 + 31 32 1 0.330 5000 + 32 33 1 0.380 5000 + 34 35 1 0.336 7500 + 39 40 1 0.363 7500 + 41 42 1 0.352 7500 + 43 44 1 0.352 5000 + 45 46 1 0.325 5000 + 50 51 1 0.330 5000 + 51 52 1 0.380 5000 + 54 55 1 0.325 5000 + 59 60 1 0.287 7500 + 61 62 1 0.363 7500 + 64 65 1 0.352 5000 + 66 67 1 0.315 5000 + 74 75 1 0.341 7500 + 80 81 1 0.330 5000 + 81 82 1 0.360 5000 + 83 84 1 0.325 7500 + 87 88 1 0.400 5000 + 89 90 1 0.287 7500 + 91 92 1 0.352 5000 + 93 94 1 0.325 7500 + 97 98 1 0.352 5000 +101 102 1 0.400 5000 +107 108 1 0.352 5000 +109 110 1 0.330 5000 +110 111 1 0.380 5000 +112 113 1 0.352 5000 +116 117 1 0.352 7500 +119 120 1 0.287 7500 +123 124 1 0.352 7500 +125 126 1 0.325 5000 +133 134 1 0.363 7500 +135 136 1 0.400 5000 +139 140 1 0.352 5000 +141 142 1 0.287 7500 +143 144 1 0.330 5000 +144 145 1 0.380 5000 +146 147 1 0.315 5000 +152 153 1 0.315 5000 +158 159 1 0.341 7500 +160 161 1 0.352 5000 +162 163 1 0.352 7500 +165 166 1 0.330 5000 +166 167 1 0.380 5000 +170 171 1 0.330 7500 +173 174 1 0.287 7500 +175 176 1 0.330 5000 +176 177 1 0.380 5000 +178 179 1 0.352 5000 +180 181 1 0.363 7500 +182 183 1 0.341 7500 +184 185 1 0.352 5000 +188 189 1 0.330 7500 +190 191 1 0.341 7500 +192 193 1 0.287 7500 +196 197 1 0.363 7500 +198 199 1 0.363 7500 +200 201 1 0.287 7500 +202 203 1 0.287 7500 +204 205 1 0.352 7500 +212 213 1 0.287 7500 +216 217 1 0.352 5000 +218 219 1 0.341 7500 +222 223 1 0.330 5000 +223 224 1 0.360 5000 +225 226 1 0.330 5000 +226 227 1 0.360 5000 +232 233 1 0.287 7500 +234 235 1 0.352 7500 +237 238 1 0.352 5000 +240 241 1 0.40 2500 +242 243 1 0.352 5000 +246 247 1 0.315 5000 +256 257 1 0.315 5000 +262 263 1 0.330 5000 +263 264 1 0.380 5000 +265 266 1 0.352 5000 +267 268 1 0.330 5000 +268 269 1 0.380 5000 +270 271 1 0.341 7500 +272 273 1 0.330 5000 +273 274 1 0.360 5000 +278 279 1 0.352 7500 +282 283 1 0.400 5000 +286 287 1 0.315 5000 +294 295 1 0.330 5000 +295 296 1 0.380 5000 +298 299 1 0.341 7500 +300 301 1 0.330 5000 +301 302 1 0.380 5000 +303 304 1 0.363 7500 + +#ifdef FLEXIBLE +; Side chain bonds + 4 5 1 0.292 1000000 + 7 8 1 0.340 1000000 + 7 9 1 0.340 1000000 + 8 9 1 0.290 1000000 + 20 21 1 0.270 1000000 + 22 23 1 0.270 1000000 + 24 25 1 0.270 1000000 + 35 36 1 0.320 1000000 + 35 37 1 0.300 1000000 + 36 37 1 0.270 1000000 + 46 47 1 0.300 1000000 + 46 48 1 0.300 1000000 + 47 49 1 0.285 1000000 + 48 49 1 0.285 1000000 + 47 48 1 0.300 1000000 + 55 56 1 0.300 1000000 + 55 57 1 0.300 1000000 + 56 58 1 0.285 1000000 + 57 58 1 0.285 1000000 + 56 57 1 0.300 1000000 + 67 68 1 0.335 1000000 + 68 71 1 0.412 1000000 + 70 71 1 0.293 1000000 + 67 70 1 0.404 1000000 + 68 70 1 0.470 1000000 + 72 73 1 0.292 1000000 + 76 77 1 0.270 1000000 + 78 79 1 0.270 1000000 + 84 85 1 0.340 1000000 + 84 86 1 0.340 1000000 + 85 86 1 0.290 1000000 + 94 95 1 0.340 1000000 + 94 96 1 0.340 1000000 + 95 96 1 0.290 1000000 + 99 100 1 0.305 1000000 +103 104 1 0.270 1000000 +105 106 1 0.305 1000000 +114 115 1 0.305 1000000 +121 122 1 0.305 1000000 +126 127 1 0.300 1000000 +126 128 1 0.300 1000000 +127 129 1 0.285 1000000 +128 129 1 0.285 1000000 +127 128 1 0.300 1000000 +131 132 1 0.341 1000000 +137 138 1 0.341 1000000 +147 148 1 0.335 1000000 +148 151 1 0.412 1000000 +150 151 1 0.293 1000000 +147 150 1 0.404 1000000 +148 150 1 0.470 1000000 +153 154 1 0.335 1000000 +154 157 1 0.412 1000000 +156 157 1 0.293 1000000 +153 156 1 0.404 1000000 +154 156 1 0.470 1000000 +168 169 1 0.305 1000000 +186 187 1 0.341 1000000 +194 195 1 0.270 1000000 +206 207 1 0.341 1000000 +208 209 1 0.305 1000000 +210 211 1 0.270 1000000 +214 215 1 0.292 1000000 +220 221 1 0.270 1000000 +228 229 1 0.341 1000000 +230 231 1 0.292 1000000 +244 245 1 0.270 1000000 +247 248 1 0.335 1000000 +248 251 1 0.412 1000000 +250 251 1 0.293 1000000 +247 250 1 0.404 1000000 +248 250 1 0.470 1000000 +252 253 1 0.292 1000000 +254 255 1 0.270 1000000 +257 258 1 0.335 1000000 +258 261 1 0.412 1000000 +260 261 1 0.293 1000000 +257 260 1 0.404 1000000 +258 260 1 0.470 1000000 +276 277 1 0.305 1000000 +280 281 1 0.292 1000000 +284 285 1 0.270 1000000 +287 288 1 0.335 1000000 +288 291 1 0.412 1000000 +290 291 1 0.293 1000000 +287 290 1 0.404 1000000 +288 290 1 0.470 1000000 +292 293 1 0.341 1000000 +#endif + +[ constraints ] + 15 299 1 0.24 ; Disulfide bridge + 75 271 1 0.24 ; Disulfide bridge +159 191 1 0.24 ; Disulfide bridge +183 219 1 0.24 ; Disulfide bridge + +; Backbone bonds + 10 11 1 0.33 + 11 14 1 0.310 + 14 16 1 0.310 + 16 18 1 0.310 + 18 20 1 0.310 + 20 22 1 0.310 + 22 24 1 0.310 + 24 26 1 0.310 + 26 28 1 0.310 + 28 31 1 0.310 + 31 34 1 0.33 + 59 61 1 0.33 + 61 63 1 0.310 + 63 64 1 0.310 + 64 66 1 0.310 + 66 72 1 0.310 + 72 74 1 0.310 + 74 76 1 0.310 + 76 78 1 0.310 + 78 80 1 0.310 + 80 83 1 0.310 + 83 87 1 0.310 + 87 89 1 0.310 + 89 91 1 0.33 +188 190 1 0.33 +190 192 1 0.310 +192 194 1 0.310 +194 196 1 0.310 +196 198 1 0.310 +198 200 1 0.33 +206 208 1 0.33 +208 210 1 0.310 +210 212 1 0.310 +212 214 1 0.310 +214 216 1 0.310 +216 218 1 0.310 +218 220 1 0.310 +220 222 1 0.310 +222 225 1 0.310 +225 228 1 0.310 +228 230 1 0.310 +230 232 1 0.310 +232 234 1 0.33 +237 239 1 0.33 +239 240 1 0.310 +240 242 1 0.310 +242 244 1 0.310 +244 246 1 0.33 +246 252 1 0.33 +252 254 1 0.310 +254 256 1 0.310 +256 262 1 0.310 +262 265 1 0.310 +265 267 1 0.310 +267 270 1 0.33 +278 280 1 0.33 +280 282 1 0.310 +282 284 1 0.310 +284 286 1 0.310 +286 292 1 0.310 +292 294 1 0.33 + +#ifndef FLEXIBLE +; Side chain bonds + 4 5 1 0.292 + 7 8 1 0.340 + 7 9 1 0.340 + 8 9 1 0.290 + 20 21 1 0.270 + 22 23 1 0.270 + 24 25 1 0.270 + 35 36 1 0.320 + 35 37 1 0.300 + 36 37 1 0.270 + 46 47 1 0.300 + 46 48 1 0.300 + 47 49 1 0.285 + 48 49 1 0.285 + 47 48 1 0.300 + 55 56 1 0.300 + 55 57 1 0.300 + 56 58 1 0.285 + 57 58 1 0.285 + 56 57 1 0.300 + 67 68 1 0.335 + 68 71 1 0.412 + 70 71 1 0.293 + 67 70 1 0.404 + 68 70 1 0.470 + 72 73 1 0.292 + 76 77 1 0.270 + 78 79 1 0.270 + 84 85 1 0.340 + 84 86 1 0.340 + 85 86 1 0.290 + 94 95 1 0.340 + 94 96 1 0.340 + 95 96 1 0.290 + 99 100 1 0.305 +103 104 1 0.270 +105 106 1 0.305 +114 115 1 0.305 +121 122 1 0.305 +126 127 1 0.300 +126 128 1 0.300 +127 129 1 0.285 +128 129 1 0.285 +127 128 1 0.300 +131 132 1 0.341 +137 138 1 0.341 +147 148 1 0.335 +148 151 1 0.412 +150 151 1 0.293 +147 150 1 0.404 +148 150 1 0.470 +153 154 1 0.335 +154 157 1 0.412 +156 157 1 0.293 +153 156 1 0.404 +154 156 1 0.470 +168 169 1 0.305 +186 187 1 0.341 +194 195 1 0.270 +206 207 1 0.341 +208 209 1 0.305 +210 211 1 0.270 +214 215 1 0.292 +220 221 1 0.270 +228 229 1 0.341 +230 231 1 0.292 +244 245 1 0.270 +247 248 1 0.335 +248 251 1 0.412 +250 251 1 0.293 +247 250 1 0.404 +248 250 1 0.470 +252 253 1 0.292 +254 255 1 0.270 +257 258 1 0.335 +258 261 1 0.412 +260 261 1 0.293 +257 260 1 0.404 +258 260 1 0.470 +276 277 1 0.305 +280 281 1 0.292 +284 285 1 0.270 +287 288 1 0.335 +288 291 1 0.412 +290 291 1 0.293 +287 290 1 0.404 +288 290 1 0.470 +292 293 1 0.341 +#endif + +[ angles ] +; BBB angles + 6 10 11 10 127 20 + 10 11 14 10 127 20 + 11 14 16 2 96 700 + 14 16 18 2 96 700 + 16 18 20 2 96 700 + 18 20 22 2 96 700 + 20 22 24 2 96 700 + 22 24 26 2 96 700 + 24 26 28 2 96 700 + 26 28 31 2 96 700 + 28 31 34 10 100 20 + 31 34 38 10 100 20 + 54 59 61 10 127 20 + 59 61 63 10 127 20 + 61 63 64 2 96 700 + 63 64 66 2 96 700 + 64 66 72 2 96 700 + 66 72 74 2 96 700 + 72 74 76 2 96 700 + 74 76 78 2 96 700 + 76 78 80 2 96 700 + 78 80 83 2 96 700 + 80 83 87 2 96 700 + 83 87 89 2 96 700 + 87 89 91 10 100 20 + 89 91 93 10 100 20 +186 188 190 10 130 20 +188 190 192 10 134 25 +190 192 194 2 96 700 +192 194 196 2 96 700 +194 196 198 2 96 700 +196 198 200 10 130 20 +198 200 202 10 130 20 +204 206 208 10 127 20 +206 208 210 10 127 20 +208 210 212 2 96 700 +210 212 214 2 96 700 +212 214 216 2 96 700 +214 216 218 2 96 700 +216 218 220 2 96 700 +218 220 222 2 96 700 +220 222 225 2 96 700 +222 225 228 2 96 700 +225 228 230 2 96 700 +228 230 232 2 96 700 +230 232 234 10 100 20 +232 234 236 10 100 20 +236 237 239 10 130 20 +237 239 240 10 130 20 +239 240 242 2 96 700 +240 242 244 2 96 700 +242 244 246 10 130 20 +244 246 252 10 130 20 +246 252 254 10 130 20 +252 254 256 2 96 700 +254 256 262 2 96 700 +256 262 265 2 96 700 +262 265 267 2 96 700 +265 267 270 10 100 20 +267 270 272 10 100 20 +276 278 280 10 127 20 +278 280 282 10 127 20 +280 282 284 2 96 700 +282 284 286 2 96 700 +284 286 292 2 96 700 +286 292 294 10 100 20 +292 294 297 10 100 20 + 1 4 6 10 127 20 + 4 6 10 10 127 20 + 41 43 45 10 100 20 + 43 45 50 10 100 20 + 45 50 53 10 100 20 + 50 53 54 10 100 20 + 53 54 59 10 100 20 + 91 93 97 10 100 20 + 93 97 99 10 100 20 + 97 99 101 10 100 20 +101 103 105 10 100 20 +103 105 107 10 127 20 +105 107 109 10 134 25 +107 109 112 10 127 20 +109 112 114 10 100 20 +118 119 121 10 127 20 +119 121 123 10 127 20 +121 123 125 10 134 25 +123 125 130 10 100 20 +125 130 131 10 100 20 +133 135 137 10 100 20 +135 137 139 10 100 20 +137 139 141 10 100 20 +139 141 143 10 100 20 +152 158 160 10 100 20 +158 160 162 10 127 20 +160 162 164 10 127 20 +184 186 188 10 127 20 +165 168 170 10 127 20 +168 170 172 10 100 20 +170 172 173 10 100 20 +114 116 118 10 100 20 +116 118 119 10 100 20 +162 164 165 10 127 20 +164 165 168 10 127 20 +182 184 186 10 100 20 +200 202 204 10 130 20 +202 204 206 10 127 20 +234 236 237 10 100 20 +272 275 276 10 100 20 +275 276 278 10 100 20 + 34 38 39 10 100 20 + 38 39 41 10 100 20 + 39 41 43 10 100 20 + 99 101 103 10 100 20 +112 114 116 10 100 20 +146 152 158 10 100 20 +172 173 175 10 100 20 +173 175 178 10 127 20 +175 178 180 10 100 20 +178 180 182 10 100 20 +180 182 184 10 100 20 +294 297 298 10 100 20 +297 298 300 10 100 20 +298 300 303 10 127 20 +130 131 133 10 100 20 +131 133 135 10 100 20 +141 143 146 10 100 20 +143 146 152 10 100 20 +270 272 275 10 100 20 + +; BBS angles regular martini + 1 4 5 2 100 25 + 4 6 7 2 100 25 + 10 11 12 2 100 25 + 11 14 15 2 100 25 + 14 16 17 2 100 25 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250 248 247 2 180.0 100.0 +261 260 258 257 2 180.0 100.0 +291 290 288 287 2 180.0 100.0 + +[ virtual_sitesn ] + 69 2 71 70 68 67 +149 2 151 150 148 147 +155 2 157 156 154 153 +249 2 251 250 248 247 +259 2 261 260 258 257 +289 2 291 290 288 287 + +; Virtual go site +305 1 1 +306 1 4 +307 1 6 +308 1 10 +309 1 11 +310 1 14 +311 1 16 +312 1 18 +313 1 20 +314 1 22 +315 1 24 +316 1 26 +317 1 28 +318 1 31 +319 1 34 +320 1 38 +321 1 39 +322 1 41 +323 1 43 +324 1 45 +325 1 50 +326 1 53 +327 1 54 +328 1 59 +329 1 61 +330 1 63 +331 1 64 +332 1 66 +333 1 72 +334 1 74 +335 1 76 +336 1 78 +337 1 80 +338 1 83 +339 1 87 +340 1 89 +341 1 91 +342 1 93 +343 1 97 +344 1 99 +345 1 101 +346 1 103 +347 1 105 +348 1 107 +349 1 109 +350 1 112 +351 1 114 +352 1 116 +353 1 118 +354 1 119 +355 1 121 +356 1 123 +357 1 125 +358 1 130 +359 1 131 +360 1 133 +361 1 135 +362 1 137 +363 1 139 +364 1 141 +365 1 143 +366 1 146 +367 1 152 +368 1 158 +369 1 160 +370 1 162 +371 1 164 +372 1 165 +373 1 168 +374 1 170 +375 1 172 +376 1 173 +377 1 175 +378 1 178 +379 1 180 +380 1 182 +381 1 184 +382 1 186 +383 1 188 +384 1 190 +385 1 192 +386 1 194 +387 1 196 +388 1 198 +389 1 200 +390 1 202 +391 1 204 +392 1 206 +393 1 208 +394 1 210 +395 1 212 +396 1 214 +397 1 216 +398 1 218 +399 1 220 +400 1 222 +401 1 225 +402 1 228 +403 1 230 +404 1 232 +405 1 234 +406 1 236 +407 1 237 +408 1 239 +409 1 240 +410 1 242 +411 1 244 +412 1 246 +413 1 252 +414 1 254 +415 1 256 +416 1 262 +417 1 265 +418 1 267 +419 1 270 +420 1 272 +421 1 275 +422 1 276 +423 1 278 +424 1 280 +425 1 282 +426 1 284 +427 1 286 +428 1 292 +429 1 294 +430 1 297 +431 1 298 +432 1 300 +433 1 303 + From b4f3d1475ad344da535a6f05707839149e48a90a Mon Sep 17 00:00:00 2001 From: csbrasnett Date: Mon, 28 Oct 2024 14:32:45 +0100 Subject: [PATCH 6/6] redid tests to fix and ensure coverage --- .../tier-1/lysozyme_GO/martinize2/command | 1 + .../lysozyme_GO/martinize2/go_atomtypes.itp | 258 +-- .../lysozyme_GO/martinize2/go_nbparams.itp | 518 ++--- .../{molecule.itp => molecule_0.itp} | 875 ++++--- .../tier-1/lysozyme_GO/martinize2/topol.top | 4 +- .../tier-1/lysozyme_GObias/martinize2/command | 1 + .../martinize2/go_atomtypes.itp | 258 +-- .../martinize2/go_nbparams.itp | 596 ++--- .../lysozyme_GObias/martinize2/molecule.itp | 2027 ----------------- .../lysozyme_GObias/martinize2/molecule_0.itp | 1669 ++++++++++++++ .../lysozyme_GObias/martinize2/topol.top | 4 +- 11 files changed, 2933 insertions(+), 3278 deletions(-) rename vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/{molecule.itp => molecule_0.itp} (51%) delete mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command index cdf208511..a0e75009d 100755 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command @@ -8,3 +8,4 @@ martinize2 -go ../map.map -noscfix -cys none +-name molecule_0 \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp index 3b028c477..bcbcf6145 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp @@ -1,130 +1,130 @@ [ atomtypes ] -molecule_1 0.0 0 A 0.00000000 0.00000000 -molecule_2 0.0 0 A 0.00000000 0.00000000 -molecule_3 0.0 0 A 0.00000000 0.00000000 -molecule_4 0.0 0 A 0.00000000 0.00000000 -molecule_5 0.0 0 A 0.00000000 0.00000000 -molecule_6 0.0 0 A 0.00000000 0.00000000 -molecule_7 0.0 0 A 0.00000000 0.00000000 -molecule_8 0.0 0 A 0.00000000 0.00000000 -molecule_9 0.0 0 A 0.00000000 0.00000000 -molecule_10 0.0 0 A 0.00000000 0.00000000 -molecule_11 0.0 0 A 0.00000000 0.00000000 -molecule_12 0.0 0 A 0.00000000 0.00000000 -molecule_13 0.0 0 A 0.00000000 0.00000000 -molecule_14 0.0 0 A 0.00000000 0.00000000 -molecule_15 0.0 0 A 0.00000000 0.00000000 -molecule_16 0.0 0 A 0.00000000 0.00000000 -molecule_17 0.0 0 A 0.00000000 0.00000000 -molecule_18 0.0 0 A 0.00000000 0.00000000 -molecule_19 0.0 0 A 0.00000000 0.00000000 -molecule_20 0.0 0 A 0.00000000 0.00000000 -molecule_21 0.0 0 A 0.00000000 0.00000000 -molecule_22 0.0 0 A 0.00000000 0.00000000 -molecule_23 0.0 0 A 0.00000000 0.00000000 -molecule_24 0.0 0 A 0.00000000 0.00000000 -molecule_25 0.0 0 A 0.00000000 0.00000000 -molecule_26 0.0 0 A 0.00000000 0.00000000 -molecule_27 0.0 0 A 0.00000000 0.00000000 -molecule_28 0.0 0 A 0.00000000 0.00000000 -molecule_29 0.0 0 A 0.00000000 0.00000000 -molecule_30 0.0 0 A 0.00000000 0.00000000 -molecule_31 0.0 0 A 0.00000000 0.00000000 -molecule_32 0.0 0 A 0.00000000 0.00000000 -molecule_33 0.0 0 A 0.00000000 0.00000000 -molecule_34 0.0 0 A 0.00000000 0.00000000 -molecule_35 0.0 0 A 0.00000000 0.00000000 -molecule_36 0.0 0 A 0.00000000 0.00000000 -molecule_37 0.0 0 A 0.00000000 0.00000000 -molecule_38 0.0 0 A 0.00000000 0.00000000 -molecule_39 0.0 0 A 0.00000000 0.00000000 -molecule_40 0.0 0 A 0.00000000 0.00000000 -molecule_41 0.0 0 A 0.00000000 0.00000000 -molecule_42 0.0 0 A 0.00000000 0.00000000 -molecule_43 0.0 0 A 0.00000000 0.00000000 -molecule_44 0.0 0 A 0.00000000 0.00000000 -molecule_45 0.0 0 A 0.00000000 0.00000000 -molecule_46 0.0 0 A 0.00000000 0.00000000 -molecule_47 0.0 0 A 0.00000000 0.00000000 -molecule_48 0.0 0 A 0.00000000 0.00000000 -molecule_49 0.0 0 A 0.00000000 0.00000000 -molecule_50 0.0 0 A 0.00000000 0.00000000 -molecule_51 0.0 0 A 0.00000000 0.00000000 -molecule_52 0.0 0 A 0.00000000 0.00000000 -molecule_53 0.0 0 A 0.00000000 0.00000000 -molecule_54 0.0 0 A 0.00000000 0.00000000 -molecule_55 0.0 0 A 0.00000000 0.00000000 -molecule_56 0.0 0 A 0.00000000 0.00000000 -molecule_57 0.0 0 A 0.00000000 0.00000000 -molecule_58 0.0 0 A 0.00000000 0.00000000 -molecule_59 0.0 0 A 0.00000000 0.00000000 -molecule_60 0.0 0 A 0.00000000 0.00000000 -molecule_61 0.0 0 A 0.00000000 0.00000000 -molecule_62 0.0 0 A 0.00000000 0.00000000 -molecule_63 0.0 0 A 0.00000000 0.00000000 -molecule_64 0.0 0 A 0.00000000 0.00000000 -molecule_65 0.0 0 A 0.00000000 0.00000000 -molecule_66 0.0 0 A 0.00000000 0.00000000 -molecule_67 0.0 0 A 0.00000000 0.00000000 -molecule_68 0.0 0 A 0.00000000 0.00000000 -molecule_69 0.0 0 A 0.00000000 0.00000000 -molecule_70 0.0 0 A 0.00000000 0.00000000 -molecule_71 0.0 0 A 0.00000000 0.00000000 -molecule_72 0.0 0 A 0.00000000 0.00000000 -molecule_73 0.0 0 A 0.00000000 0.00000000 -molecule_74 0.0 0 A 0.00000000 0.00000000 -molecule_75 0.0 0 A 0.00000000 0.00000000 -molecule_76 0.0 0 A 0.00000000 0.00000000 -molecule_77 0.0 0 A 0.00000000 0.00000000 -molecule_78 0.0 0 A 0.00000000 0.00000000 -molecule_79 0.0 0 A 0.00000000 0.00000000 -molecule_80 0.0 0 A 0.00000000 0.00000000 -molecule_81 0.0 0 A 0.00000000 0.00000000 -molecule_82 0.0 0 A 0.00000000 0.00000000 -molecule_83 0.0 0 A 0.00000000 0.00000000 -molecule_84 0.0 0 A 0.00000000 0.00000000 -molecule_85 0.0 0 A 0.00000000 0.00000000 -molecule_86 0.0 0 A 0.00000000 0.00000000 -molecule_87 0.0 0 A 0.00000000 0.00000000 -molecule_88 0.0 0 A 0.00000000 0.00000000 -molecule_89 0.0 0 A 0.00000000 0.00000000 -molecule_90 0.0 0 A 0.00000000 0.00000000 -molecule_91 0.0 0 A 0.00000000 0.00000000 -molecule_92 0.0 0 A 0.00000000 0.00000000 -molecule_93 0.0 0 A 0.00000000 0.00000000 -molecule_94 0.0 0 A 0.00000000 0.00000000 -molecule_95 0.0 0 A 0.00000000 0.00000000 -molecule_96 0.0 0 A 0.00000000 0.00000000 -molecule_97 0.0 0 A 0.00000000 0.00000000 -molecule_98 0.0 0 A 0.00000000 0.00000000 -molecule_99 0.0 0 A 0.00000000 0.00000000 -molecule_100 0.0 0 A 0.00000000 0.00000000 -molecule_101 0.0 0 A 0.00000000 0.00000000 -molecule_102 0.0 0 A 0.00000000 0.00000000 -molecule_103 0.0 0 A 0.00000000 0.00000000 -molecule_104 0.0 0 A 0.00000000 0.00000000 -molecule_105 0.0 0 A 0.00000000 0.00000000 -molecule_106 0.0 0 A 0.00000000 0.00000000 -molecule_107 0.0 0 A 0.00000000 0.00000000 -molecule_108 0.0 0 A 0.00000000 0.00000000 -molecule_109 0.0 0 A 0.00000000 0.00000000 -molecule_110 0.0 0 A 0.00000000 0.00000000 -molecule_111 0.0 0 A 0.00000000 0.00000000 -molecule_112 0.0 0 A 0.00000000 0.00000000 -molecule_113 0.0 0 A 0.00000000 0.00000000 -molecule_114 0.0 0 A 0.00000000 0.00000000 -molecule_115 0.0 0 A 0.00000000 0.00000000 -molecule_116 0.0 0 A 0.00000000 0.00000000 -molecule_117 0.0 0 A 0.00000000 0.00000000 -molecule_118 0.0 0 A 0.00000000 0.00000000 -molecule_119 0.0 0 A 0.00000000 0.00000000 -molecule_120 0.0 0 A 0.00000000 0.00000000 -molecule_121 0.0 0 A 0.00000000 0.00000000 -molecule_122 0.0 0 A 0.00000000 0.00000000 -molecule_123 0.0 0 A 0.00000000 0.00000000 -molecule_124 0.0 0 A 0.00000000 0.00000000 -molecule_125 0.0 0 A 0.00000000 0.00000000 -molecule_126 0.0 0 A 0.00000000 0.00000000 -molecule_127 0.0 0 A 0.00000000 0.00000000 -molecule_128 0.0 0 A 0.00000000 0.00000000 -molecule_129 0.0 0 A 0.00000000 0.00000000 +molecule_0_1 0.0 0 A 0.00000000 0.00000000 +molecule_0_2 0.0 0 A 0.00000000 0.00000000 +molecule_0_3 0.0 0 A 0.00000000 0.00000000 +molecule_0_4 0.0 0 A 0.00000000 0.00000000 +molecule_0_5 0.0 0 A 0.00000000 0.00000000 +molecule_0_6 0.0 0 A 0.00000000 0.00000000 +molecule_0_7 0.0 0 A 0.00000000 0.00000000 +molecule_0_8 0.0 0 A 0.00000000 0.00000000 +molecule_0_9 0.0 0 A 0.00000000 0.00000000 +molecule_0_10 0.0 0 A 0.00000000 0.00000000 +molecule_0_11 0.0 0 A 0.00000000 0.00000000 +molecule_0_12 0.0 0 A 0.00000000 0.00000000 +molecule_0_13 0.0 0 A 0.00000000 0.00000000 +molecule_0_14 0.0 0 A 0.00000000 0.00000000 +molecule_0_15 0.0 0 A 0.00000000 0.00000000 +molecule_0_16 0.0 0 A 0.00000000 0.00000000 +molecule_0_17 0.0 0 A 0.00000000 0.00000000 +molecule_0_18 0.0 0 A 0.00000000 0.00000000 +molecule_0_19 0.0 0 A 0.00000000 0.00000000 +molecule_0_20 0.0 0 A 0.00000000 0.00000000 +molecule_0_21 0.0 0 A 0.00000000 0.00000000 +molecule_0_22 0.0 0 A 0.00000000 0.00000000 +molecule_0_23 0.0 0 A 0.00000000 0.00000000 +molecule_0_24 0.0 0 A 0.00000000 0.00000000 +molecule_0_25 0.0 0 A 0.00000000 0.00000000 +molecule_0_26 0.0 0 A 0.00000000 0.00000000 +molecule_0_27 0.0 0 A 0.00000000 0.00000000 +molecule_0_28 0.0 0 A 0.00000000 0.00000000 +molecule_0_29 0.0 0 A 0.00000000 0.00000000 +molecule_0_30 0.0 0 A 0.00000000 0.00000000 +molecule_0_31 0.0 0 A 0.00000000 0.00000000 +molecule_0_32 0.0 0 A 0.00000000 0.00000000 +molecule_0_33 0.0 0 A 0.00000000 0.00000000 +molecule_0_34 0.0 0 A 0.00000000 0.00000000 +molecule_0_35 0.0 0 A 0.00000000 0.00000000 +molecule_0_36 0.0 0 A 0.00000000 0.00000000 +molecule_0_37 0.0 0 A 0.00000000 0.00000000 +molecule_0_38 0.0 0 A 0.00000000 0.00000000 +molecule_0_39 0.0 0 A 0.00000000 0.00000000 +molecule_0_40 0.0 0 A 0.00000000 0.00000000 +molecule_0_41 0.0 0 A 0.00000000 0.00000000 +molecule_0_42 0.0 0 A 0.00000000 0.00000000 +molecule_0_43 0.0 0 A 0.00000000 0.00000000 +molecule_0_44 0.0 0 A 0.00000000 0.00000000 +molecule_0_45 0.0 0 A 0.00000000 0.00000000 +molecule_0_46 0.0 0 A 0.00000000 0.00000000 +molecule_0_47 0.0 0 A 0.00000000 0.00000000 +molecule_0_48 0.0 0 A 0.00000000 0.00000000 +molecule_0_49 0.0 0 A 0.00000000 0.00000000 +molecule_0_50 0.0 0 A 0.00000000 0.00000000 +molecule_0_51 0.0 0 A 0.00000000 0.00000000 +molecule_0_52 0.0 0 A 0.00000000 0.00000000 +molecule_0_53 0.0 0 A 0.00000000 0.00000000 +molecule_0_54 0.0 0 A 0.00000000 0.00000000 +molecule_0_55 0.0 0 A 0.00000000 0.00000000 +molecule_0_56 0.0 0 A 0.00000000 0.00000000 +molecule_0_57 0.0 0 A 0.00000000 0.00000000 +molecule_0_58 0.0 0 A 0.00000000 0.00000000 +molecule_0_59 0.0 0 A 0.00000000 0.00000000 +molecule_0_60 0.0 0 A 0.00000000 0.00000000 +molecule_0_61 0.0 0 A 0.00000000 0.00000000 +molecule_0_62 0.0 0 A 0.00000000 0.00000000 +molecule_0_63 0.0 0 A 0.00000000 0.00000000 +molecule_0_64 0.0 0 A 0.00000000 0.00000000 +molecule_0_65 0.0 0 A 0.00000000 0.00000000 +molecule_0_66 0.0 0 A 0.00000000 0.00000000 +molecule_0_67 0.0 0 A 0.00000000 0.00000000 +molecule_0_68 0.0 0 A 0.00000000 0.00000000 +molecule_0_69 0.0 0 A 0.00000000 0.00000000 +molecule_0_70 0.0 0 A 0.00000000 0.00000000 +molecule_0_71 0.0 0 A 0.00000000 0.00000000 +molecule_0_72 0.0 0 A 0.00000000 0.00000000 +molecule_0_73 0.0 0 A 0.00000000 0.00000000 +molecule_0_74 0.0 0 A 0.00000000 0.00000000 +molecule_0_75 0.0 0 A 0.00000000 0.00000000 +molecule_0_76 0.0 0 A 0.00000000 0.00000000 +molecule_0_77 0.0 0 A 0.00000000 0.00000000 +molecule_0_78 0.0 0 A 0.00000000 0.00000000 +molecule_0_79 0.0 0 A 0.00000000 0.00000000 +molecule_0_80 0.0 0 A 0.00000000 0.00000000 +molecule_0_81 0.0 0 A 0.00000000 0.00000000 +molecule_0_82 0.0 0 A 0.00000000 0.00000000 +molecule_0_83 0.0 0 A 0.00000000 0.00000000 +molecule_0_84 0.0 0 A 0.00000000 0.00000000 +molecule_0_85 0.0 0 A 0.00000000 0.00000000 +molecule_0_86 0.0 0 A 0.00000000 0.00000000 +molecule_0_87 0.0 0 A 0.00000000 0.00000000 +molecule_0_88 0.0 0 A 0.00000000 0.00000000 +molecule_0_89 0.0 0 A 0.00000000 0.00000000 +molecule_0_90 0.0 0 A 0.00000000 0.00000000 +molecule_0_91 0.0 0 A 0.00000000 0.00000000 +molecule_0_92 0.0 0 A 0.00000000 0.00000000 +molecule_0_93 0.0 0 A 0.00000000 0.00000000 +molecule_0_94 0.0 0 A 0.00000000 0.00000000 +molecule_0_95 0.0 0 A 0.00000000 0.00000000 +molecule_0_96 0.0 0 A 0.00000000 0.00000000 +molecule_0_97 0.0 0 A 0.00000000 0.00000000 +molecule_0_98 0.0 0 A 0.00000000 0.00000000 +molecule_0_99 0.0 0 A 0.00000000 0.00000000 +molecule_0_100 0.0 0 A 0.00000000 0.00000000 +molecule_0_101 0.0 0 A 0.00000000 0.00000000 +molecule_0_102 0.0 0 A 0.00000000 0.00000000 +molecule_0_103 0.0 0 A 0.00000000 0.00000000 +molecule_0_104 0.0 0 A 0.00000000 0.00000000 +molecule_0_105 0.0 0 A 0.00000000 0.00000000 +molecule_0_106 0.0 0 A 0.00000000 0.00000000 +molecule_0_107 0.0 0 A 0.00000000 0.00000000 +molecule_0_108 0.0 0 A 0.00000000 0.00000000 +molecule_0_109 0.0 0 A 0.00000000 0.00000000 +molecule_0_110 0.0 0 A 0.00000000 0.00000000 +molecule_0_111 0.0 0 A 0.00000000 0.00000000 +molecule_0_112 0.0 0 A 0.00000000 0.00000000 +molecule_0_113 0.0 0 A 0.00000000 0.00000000 +molecule_0_114 0.0 0 A 0.00000000 0.00000000 +molecule_0_115 0.0 0 A 0.00000000 0.00000000 +molecule_0_116 0.0 0 A 0.00000000 0.00000000 +molecule_0_117 0.0 0 A 0.00000000 0.00000000 +molecule_0_118 0.0 0 A 0.00000000 0.00000000 +molecule_0_119 0.0 0 A 0.00000000 0.00000000 +molecule_0_120 0.0 0 A 0.00000000 0.00000000 +molecule_0_121 0.0 0 A 0.00000000 0.00000000 +molecule_0_122 0.0 0 A 0.00000000 0.00000000 +molecule_0_123 0.0 0 A 0.00000000 0.00000000 +molecule_0_124 0.0 0 A 0.00000000 0.00000000 +molecule_0_125 0.0 0 A 0.00000000 0.00000000 +molecule_0_126 0.0 0 A 0.00000000 0.00000000 +molecule_0_127 0.0 0 A 0.00000000 0.00000000 +molecule_0_128 0.0 0 A 0.00000000 0.00000000 +molecule_0_129 0.0 0 A 0.00000000 0.00000000 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp index 0808f6b09..8c545698f 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp @@ -1,260 +1,260 @@ [ nonbond_params ] -molecule_7 molecule_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 -molecule_8 molecule_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 -molecule_8 molecule_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 -molecule_9 molecule_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 -molecule_10 molecule_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 -molecule_11 molecule_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 -molecule_12 molecule_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 -molecule_13 molecule_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 -molecule_14 molecule_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 -molecule_15 molecule_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 -molecule_16 molecule_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 -molecule_17 molecule_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 -molecule_18 molecule_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 -molecule_20 molecule_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 -molecule_23 molecule_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 -molecule_24 molecule_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 -molecule_24 molecule_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 -molecule_25 molecule_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 -molecule_25 molecule_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 -molecule_25 molecule_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 -molecule_25 molecule_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 -molecule_27 molecule_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 -molecule_27 molecule_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 -molecule_28 molecule_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 -molecule_28 molecule_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 -molecule_28 molecule_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 -molecule_28 molecule_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 -molecule_29 molecule_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 -molecule_29 molecule_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 -molecule_29 molecule_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 -molecule_29 molecule_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 -molecule_30 molecule_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 -molecule_31 molecule_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 -molecule_32 molecule_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 -molecule_32 molecule_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 -molecule_33 molecule_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 -molecule_34 molecule_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 -molecule_35 molecule_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 -molecule_36 molecule_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 -molecule_37 molecule_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 -molecule_37 molecule_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 -molecule_38 molecule_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 -molecule_38 molecule_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 -molecule_38 molecule_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 -molecule_38 molecule_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 -molecule_38 molecule_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 -molecule_38 molecule_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 -molecule_38 molecule_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 -molecule_38 molecule_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 -molecule_39 molecule_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 -molecule_39 molecule_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 -molecule_40 molecule_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 -molecule_40 molecule_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 -molecule_41 molecule_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 -molecule_42 molecule_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 -molecule_44 molecule_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 -molecule_49 molecule_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 -molecule_50 molecule_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 -molecule_50 molecule_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 -molecule_51 molecule_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 -molecule_51 molecule_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 -molecule_51 molecule_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 -molecule_51 molecule_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 -molecule_52 molecule_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 -molecule_52 molecule_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 -molecule_52 molecule_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 -molecule_53 molecule_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 -molecule_53 molecule_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 -molecule_54 molecule_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 -molecule_54 molecule_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 -molecule_54 molecule_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 -molecule_55 molecule_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 -molecule_55 molecule_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 -molecule_55 molecule_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 -molecule_55 molecule_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 -molecule_55 molecule_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 -molecule_55 molecule_38 1 0.53863592 9.41400000 ;go bond 0.6045983765957093 -molecule_55 molecule_39 1 0.46884965 9.41400000 ;go bond 0.5262659343028784 -molecule_55 molecule_40 1 0.49397051 9.41400000 ;go bond 0.5544631488965023 -molecule_56 molecule_31 1 0.63305577 9.41400000 ;go bond 0.7105810801311345 -molecule_56 molecule_32 1 0.57070473 9.41400000 ;go bond 0.6405943964432239 -molecule_56 molecule_35 1 0.54499611 9.41400000 ;go bond 0.6117374504966917 -molecule_57 molecule_35 1 0.59142457 9.41400000 ;go bond 0.6638516326030536 -molecule_57 molecule_36 1 0.73443635 9.41400000 ;go bond 0.8243769340599911 -molecule_57 molecule_42 1 0.68123116 9.41400000 ;go bond 0.7646561231921536 -molecule_57 molecule_43 1 0.72932038 9.41400000 ;go bond 0.8186344517277264 -molecule_57 molecule_44 1 0.71017360 9.41400000 ;go bond 0.7971429108051539 -molecule_57 molecule_52 1 0.45255106 9.41400000 ;go bond 0.5079713907835711 -molecule_57 molecule_53 1 0.35572883 9.41400000 ;go bond 0.3992921109620664 -molecule_58 molecule_52 1 0.41486867 9.41400000 ;go bond 0.4656743363160884 -molecule_58 molecule_53 1 0.33528745 9.41400000 ;go bond 0.37634743770658646 -molecule_59 molecule_46 1 0.92985190 9.41400000 ;go bond 1.0437234628284975 -molecule_59 molecule_50 1 0.67865311 9.41400000 ;go bond 0.7617623567683692 -molecule_59 molecule_51 1 0.46599015 9.41400000 ;go bond 0.5230562584392384 -molecule_59 molecule_52 1 0.52411606 9.41400000 ;go bond 0.5883003833904864 -molecule_60 molecule_50 1 0.55757626 9.41400000 ;go bond 0.6258581889054639 -molecule_60 molecule_51 1 0.45353930 9.41400000 ;go bond 0.5090806492037284 -molecule_60 molecule_53 1 0.78554721 9.41400000 ;go bond 0.8817469319963909 -molecule_61 molecule_48 1 0.83253174 9.41400000 ;go bond 0.9344852838875899 -molecule_61 molecule_50 1 0.65515556 9.41400000 ;go bond 0.7353872567523113 -molecule_63 molecule_58 1 0.62967119 9.41400000 ;go bond 0.7067820082223201 -molecule_63 molecule_59 1 0.46427561 9.41400000 ;go bond 0.521131754230626 -molecule_64 molecule_53 1 0.82959737 9.41400000 ;go bond 0.9311915604701376 -molecule_64 molecule_60 1 0.38156281 9.41400000 ;go bond 0.4282897748904594 -molecule_66 molecule_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 -molecule_66 molecule_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 -molecule_68 molecule_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 -molecule_69 molecule_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 -molecule_69 molecule_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 -molecule_69 molecule_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 -molecule_69 molecule_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 -molecule_70 molecule_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 -molecule_72 molecule_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 -molecule_72 molecule_61 1 0.44682674 9.41400000 ;go bond 0.5015460538054222 -molecule_72 molecule_64 1 0.62949829 9.41400000 ;go bond 0.7065879353028186 -molecule_73 molecule_61 1 0.53130673 9.41400000 ;go bond 0.5963716385459682 -molecule_73 molecule_62 1 0.40729971 9.41400000 ;go bond 0.4571784705977002 -molecule_74 molecule_62 1 0.44897571 9.41400000 ;go bond 0.5039581950921611 -molecule_74 molecule_63 1 0.38506256 9.41400000 ;go bond 0.43221810950469636 -molecule_74 molecule_64 1 0.43052761 9.41400000 ;go bond 0.4832509069633833 -molecule_74 molecule_65 1 0.61184241 9.41400000 ;go bond 0.6867698876930867 -molecule_75 molecule_62 1 0.52199782 9.41400000 ;go bond 0.5859227452973559 -molecule_75 molecule_63 1 0.40610455 9.41400000 ;go bond 0.45583694740556885 -molecule_76 molecule_63 1 0.46409225 9.41400000 ;go bond 0.5209259369461889 -molecule_78 molecule_63 1 0.57576077 9.41400000 ;go bond 0.6462696105707938 -molecule_78 molecule_64 1 0.45724502 9.41400000 ;go bond 0.5132401787770625 -molecule_78 molecule_65 1 0.43974215 9.41400000 ;go bond 0.4935938729629976 -molecule_78 molecule_74 1 0.56052614 9.41400000 ;go bond 0.6291693208239874 -molecule_79 molecule_64 1 0.52803406 9.41400000 ;go bond 0.5926981930678074 -molecule_79 molecule_65 1 0.39916015 9.41400000 ;go bond 0.44804212253596193 -molecule_80 molecule_53 1 0.60673469 9.41400000 ;go bond 0.6810366626079589 -molecule_80 molecule_60 1 0.73868742 9.41400000 ;go bond 0.8291485950674535 -molecule_80 molecule_64 1 0.54789421 9.41400000 ;go bond 0.6149904606975389 -molecule_80 molecule_65 1 0.47057069 9.41400000 ;go bond 0.5281977457102484 -molecule_80 molecule_66 1 0.58883652 9.41400000 ;go bond 0.6609466408239479 -molecule_82 molecule_78 1 0.66632073 9.41400000 ;go bond 0.7479197331826131 -molecule_83 molecule_53 1 0.51788905 9.41400000 ;go bond 0.581310806103053 -molecule_83 molecule_54 1 0.51088855 9.41400000 ;go bond 0.5734530137551908 -molecule_83 molecule_58 1 0.70980394 9.41400000 ;go bond 0.7967279839859979 -molecule_83 molecule_64 1 0.89499397 9.41400000 ;go bond 1.0045967605887745 -molecule_83 molecule_78 1 0.81556181 9.41400000 ;go bond 0.9154371804917103 -molecule_84 molecule_40 1 0.40226578 9.41400000 ;go bond 0.45152806893595954 -molecule_84 molecule_41 1 0.48796771 9.41400000 ;go bond 0.5477252325235119 -molecule_84 molecule_42 1 0.63252675 9.41400000 ;go bond 0.7099872721863867 -molecule_84 molecule_43 1 0.89270990 9.41400000 ;go bond 1.0020329775751635 -molecule_84 molecule_53 1 0.66502200 9.41400000 ;go bond 0.7464619538686407 -molecule_84 molecule_54 1 0.56665258 9.41400000 ;go bond 0.6360460147186728 -molecule_85 molecule_40 1 0.48170210 9.41400000 ;go bond 0.5406923273735796 -molecule_85 molecule_81 1 0.64785523 9.41400000 ;go bond 0.7271929039256984 -molecule_86 molecule_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 -molecule_86 molecule_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 -molecule_86 molecule_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 -molecule_88 molecule_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 -molecule_88 molecule_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 -molecule_88 molecule_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 -molecule_88 molecule_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 -molecule_88 molecule_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 -molecule_88 molecule_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 -molecule_89 molecule_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 -molecule_89 molecule_15 1 0.69215886 9.41400000 ;go bond 0.7769220558398894 -molecule_90 molecule_78 1 0.80563795 9.41400000 ;go bond 0.9042980239792853 -molecule_90 molecule_82 1 0.59740893 9.41400000 ;go bond 0.6705688513824994 -molecule_90 molecule_83 1 0.57714934 9.41400000 ;go bond 0.6478282257424317 -molecule_91 molecule_55 1 0.70847337 9.41400000 ;go bond 0.7952344695348353 -molecule_91 molecule_58 1 0.76773720 9.41400000 ;go bond 0.8617558647944001 -molecule_91 molecule_83 1 0.57795007 9.41400000 ;go bond 0.6487270215620753 -molecule_92 molecule_15 1 0.66057405 9.41400000 ;go bond 0.741469302181026 -molecule_92 molecule_17 1 0.76276340 9.41400000 ;go bond 0.8561729710147924 -molecule_92 molecule_88 1 0.55891711 9.41400000 ;go bond 0.6273632448163519 -molecule_93 molecule_89 1 0.55091233 9.41400000 ;go bond 0.6183781864423775 -molecule_94 molecule_58 1 0.80192436 9.41400000 ;go bond 0.9001296640477775 -molecule_94 molecule_63 1 0.69400655 9.41400000 ;go bond 0.7789960144450432 -molecule_94 molecule_76 1 0.58706169 9.41400000 ;go bond 0.6589544684537765 -molecule_94 molecule_78 1 0.87593032 9.41400000 ;go bond 0.9831985419578763 -molecule_94 molecule_83 1 0.89829847 9.41400000 ;go bond 1.0083059444227724 -molecule_94 molecule_90 1 0.53696870 9.41400000 ;go bond 0.6027269866522963 -molecule_95 molecule_28 1 0.94028879 9.41400000 ;go bond 1.0554384813372668 -molecule_95 molecule_56 1 0.76727508 9.41400000 ;go bond 0.8612371596953154 -molecule_95 molecule_58 1 0.83998475 9.41400000 ;go bond 0.9428510053550558 -molecule_95 molecule_91 1 0.53148309 9.41400000 ;go bond 0.5965695928114466 -molecule_96 molecule_15 1 0.94537258 9.41400000 ;go bond 1.0611448446580265 -molecule_96 molecule_16 1 0.84805127 9.41400000 ;go bond 0.9519053644995195 -molecule_96 molecule_17 1 0.81454872 9.41400000 ;go bond 0.9143000281459933 -molecule_96 molecule_20 1 0.73587759 9.41400000 ;go bond 0.8259946673768416 -molecule_96 molecule_92 1 0.54860993 9.41400000 ;go bond 0.6157938252917854 -molecule_97 molecule_63 1 0.84557275 9.41400000 ;go bond 0.9491233248865086 -molecule_97 molecule_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 -molecule_97 molecule_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 -molecule_98 molecule_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 -molecule_98 molecule_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 -molecule_98 molecule_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 -molecule_99 molecule_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 -molecule_99 molecule_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 -molecule_99 molecule_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 -molecule_99 molecule_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 -molecule_100 molecule_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 -molecule_100 molecule_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 -molecule_100 molecule_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 -molecule_101 molecule_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 -molecule_104 molecule_23 1 0.90496194 9.41400000 ;go bond 1.0157854279713863 -molecule_104 molecule_99 1 0.37779975 9.41400000 ;go bond 0.42406587714866395 -molecule_105 molecule_23 1 0.85792539 9.41400000 ;go bond 0.9629886926477136 -molecule_105 molecule_27 1 0.80028132 9.41400000 ;go bond 0.8982854095190085 -molecule_105 molecule_28 1 0.85914649 9.41400000 ;go bond 0.9643593287596212 -molecule_105 molecule_31 1 0.84674626 9.41400000 ;go bond 0.950440544780807 -molecule_105 molecule_99 1 0.58741430 9.41400000 ;go bond 0.6593502594081683 -molecule_107 molecule_98 1 0.70183885 9.41400000 ;go bond 0.7877874714268905 -molecule_108 molecule_28 1 0.92956079 9.41400000 ;go bond 1.0433967044744268 -molecule_108 molecule_35 1 0.82960839 9.41400000 ;go bond 0.9312039368635526 -molecule_108 molecule_56 1 0.78133210 9.41400000 ;go bond 0.8770156294387439 -molecule_108 molecule_57 1 0.77168204 9.41400000 ;go bond 0.8661838041857776 -molecule_108 molecule_98 1 0.90403083 9.41400000 ;go bond 1.014740292066367 -molecule_108 molecule_99 1 0.90315750 9.41400000 ;go bond 1.0137600206889819 -molecule_110 molecule_34 1 0.54869664 9.41400000 ;go bond 0.6158911542488904 -molecule_110 molecule_35 1 0.64980269 9.41400000 ;go bond 0.7293788607697123 -molecule_111 molecule_27 1 0.70311941 9.41400000 ;go bond 0.7892248529963473 -molecule_111 molecule_31 1 0.56259884 9.41400000 ;go bond 0.6314958500157425 -molecule_111 molecule_105 1 0.59346888 9.41400000 ;go bond 0.6661462995266982 -molecule_111 molecule_106 1 0.59882239 9.41400000 ;go bond 0.6721554100763635 -molecule_112 molecule_106 1 0.57753815 9.41400000 ;go bond 0.6482646568405853 -molecule_112 molecule_107 1 0.74260248 9.41400000 ;go bond 0.833543103918769 -molecule_112 molecule_108 1 0.53753958 9.41400000 ;go bond 0.603367775987529 -molecule_113 molecule_109 1 0.53306219 9.41400000 ;go bond 0.5983420831461288 -molecule_114 molecule_34 1 0.72771145 9.41400000 ;go bond 0.8168284821715603 -molecule_114 molecule_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 -molecule_115 molecule_30 1 0.62277169 9.41400000 ;go bond 0.6990375917289473 -molecule_115 molecule_31 1 0.71820218 9.41400000 ;go bond 0.8061546928175227 -molecule_115 molecule_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 -molecule_115 molecule_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 -molecule_115 molecule_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 -molecule_116 molecule_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 -molecule_116 molecule_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 -molecule_116 molecule_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 -molecule_118 molecule_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 -molecule_120 molecule_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 -molecule_120 molecule_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 -molecule_120 molecule_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 -molecule_120 molecule_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 -molecule_120 molecule_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 -molecule_122 molecule_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 -molecule_123 molecule_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 -molecule_123 molecule_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 -molecule_123 molecule_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 -molecule_123 molecule_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 -molecule_123 molecule_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 -molecule_123 molecule_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 -molecule_124 molecule_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 -molecule_124 molecule_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 -molecule_124 molecule_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 -molecule_124 molecule_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 -molecule_124 molecule_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 -molecule_125 molecule_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 -molecule_125 molecule_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 -molecule_127 molecule_5 1 0.79805432 9.41400000 ;go bond 0.8957856911439042 -molecule_127 molecule_6 1 0.59870073 9.41400000 ;go bond 0.6720188457372778 -molecule_129 molecule_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 -molecule_129 molecule_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 -molecule_129 molecule_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 -molecule_129 molecule_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 +molecule_0_7 molecule_0_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 +molecule_0_8 molecule_0_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 +molecule_0_8 molecule_0_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 +molecule_0_9 molecule_0_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 +molecule_0_10 molecule_0_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 +molecule_0_11 molecule_0_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 +molecule_0_12 molecule_0_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 +molecule_0_13 molecule_0_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 +molecule_0_14 molecule_0_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 +molecule_0_15 molecule_0_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 +molecule_0_16 molecule_0_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 +molecule_0_17 molecule_0_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 +molecule_0_18 molecule_0_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 +molecule_0_20 molecule_0_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 +molecule_0_23 molecule_0_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 +molecule_0_24 molecule_0_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 +molecule_0_24 molecule_0_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 +molecule_0_25 molecule_0_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 +molecule_0_25 molecule_0_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 +molecule_0_25 molecule_0_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 +molecule_0_25 molecule_0_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 +molecule_0_27 molecule_0_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 +molecule_0_27 molecule_0_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 +molecule_0_28 molecule_0_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 +molecule_0_28 molecule_0_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 +molecule_0_28 molecule_0_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 +molecule_0_28 molecule_0_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 +molecule_0_29 molecule_0_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 +molecule_0_29 molecule_0_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 +molecule_0_29 molecule_0_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 +molecule_0_29 molecule_0_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 +molecule_0_30 molecule_0_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 +molecule_0_31 molecule_0_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 +molecule_0_32 molecule_0_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 +molecule_0_32 molecule_0_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 +molecule_0_33 molecule_0_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 +molecule_0_34 molecule_0_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 +molecule_0_35 molecule_0_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 +molecule_0_36 molecule_0_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 +molecule_0_37 molecule_0_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 +molecule_0_37 molecule_0_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 +molecule_0_38 molecule_0_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 +molecule_0_38 molecule_0_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 +molecule_0_38 molecule_0_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 +molecule_0_38 molecule_0_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 +molecule_0_38 molecule_0_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 +molecule_0_38 molecule_0_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 +molecule_0_38 molecule_0_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 +molecule_0_38 molecule_0_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 +molecule_0_39 molecule_0_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 +molecule_0_39 molecule_0_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 +molecule_0_40 molecule_0_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 +molecule_0_40 molecule_0_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 +molecule_0_41 molecule_0_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 +molecule_0_42 molecule_0_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 +molecule_0_44 molecule_0_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 +molecule_0_49 molecule_0_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 +molecule_0_50 molecule_0_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 +molecule_0_50 molecule_0_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 +molecule_0_51 molecule_0_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 +molecule_0_51 molecule_0_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 +molecule_0_51 molecule_0_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 +molecule_0_51 molecule_0_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 +molecule_0_52 molecule_0_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 +molecule_0_52 molecule_0_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 +molecule_0_52 molecule_0_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 +molecule_0_53 molecule_0_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 +molecule_0_53 molecule_0_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 +molecule_0_54 molecule_0_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 +molecule_0_54 molecule_0_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 +molecule_0_54 molecule_0_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 +molecule_0_55 molecule_0_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 +molecule_0_55 molecule_0_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 +molecule_0_55 molecule_0_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 +molecule_0_55 molecule_0_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 +molecule_0_55 molecule_0_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 +molecule_0_55 molecule_0_38 1 0.53863592 9.41400000 ;go bond 0.6045983765957093 +molecule_0_55 molecule_0_39 1 0.46884965 9.41400000 ;go bond 0.5262659343028784 +molecule_0_55 molecule_0_40 1 0.49397051 9.41400000 ;go bond 0.5544631488965023 +molecule_0_56 molecule_0_31 1 0.63305577 9.41400000 ;go bond 0.7105810801311345 +molecule_0_56 molecule_0_32 1 0.57070473 9.41400000 ;go bond 0.6405943964432239 +molecule_0_56 molecule_0_35 1 0.54499611 9.41400000 ;go bond 0.6117374504966917 +molecule_0_57 molecule_0_35 1 0.59142457 9.41400000 ;go bond 0.6638516326030536 +molecule_0_57 molecule_0_36 1 0.73443635 9.41400000 ;go bond 0.8243769340599911 +molecule_0_57 molecule_0_42 1 0.68123116 9.41400000 ;go bond 0.7646561231921536 +molecule_0_57 molecule_0_43 1 0.72932038 9.41400000 ;go bond 0.8186344517277264 +molecule_0_57 molecule_0_44 1 0.71017360 9.41400000 ;go bond 0.7971429108051539 +molecule_0_57 molecule_0_52 1 0.45255106 9.41400000 ;go bond 0.5079713907835711 +molecule_0_57 molecule_0_53 1 0.35572883 9.41400000 ;go bond 0.3992921109620664 +molecule_0_58 molecule_0_52 1 0.41486867 9.41400000 ;go bond 0.4656743363160884 +molecule_0_58 molecule_0_53 1 0.33528745 9.41400000 ;go bond 0.37634743770658646 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1 0.38156281 9.41400000 ;go bond 0.4282897748904594 +molecule_0_66 molecule_0_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 +molecule_0_66 molecule_0_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 +molecule_0_68 molecule_0_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 +molecule_0_69 molecule_0_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 +molecule_0_69 molecule_0_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 +molecule_0_69 molecule_0_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 +molecule_0_69 molecule_0_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 +molecule_0_70 molecule_0_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 +molecule_0_72 molecule_0_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 +molecule_0_72 molecule_0_61 1 0.44682674 9.41400000 ;go bond 0.5015460538054222 +molecule_0_72 molecule_0_64 1 0.62949829 9.41400000 ;go bond 0.7065879353028186 +molecule_0_73 molecule_0_61 1 0.53130673 9.41400000 ;go bond 0.5963716385459682 +molecule_0_73 molecule_0_62 1 0.40729971 9.41400000 ;go bond 0.4571784705977002 +molecule_0_74 molecule_0_62 1 0.44897571 9.41400000 ;go bond 0.5039581950921611 +molecule_0_74 molecule_0_63 1 0.38506256 9.41400000 ;go bond 0.43221810950469636 +molecule_0_74 molecule_0_64 1 0.43052761 9.41400000 ;go bond 0.4832509069633833 +molecule_0_74 molecule_0_65 1 0.61184241 9.41400000 ;go bond 0.6867698876930867 +molecule_0_75 molecule_0_62 1 0.52199782 9.41400000 ;go bond 0.5859227452973559 +molecule_0_75 molecule_0_63 1 0.40610455 9.41400000 ;go bond 0.45583694740556885 +molecule_0_76 molecule_0_63 1 0.46409225 9.41400000 ;go bond 0.5209259369461889 +molecule_0_78 molecule_0_63 1 0.57576077 9.41400000 ;go bond 0.6462696105707938 +molecule_0_78 molecule_0_64 1 0.45724502 9.41400000 ;go bond 0.5132401787770625 +molecule_0_78 molecule_0_65 1 0.43974215 9.41400000 ;go bond 0.4935938729629976 +molecule_0_78 molecule_0_74 1 0.56052614 9.41400000 ;go bond 0.6291693208239874 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1 0.81556181 9.41400000 ;go bond 0.9154371804917103 +molecule_0_84 molecule_0_40 1 0.40226578 9.41400000 ;go bond 0.45152806893595954 +molecule_0_84 molecule_0_41 1 0.48796771 9.41400000 ;go bond 0.5477252325235119 +molecule_0_84 molecule_0_42 1 0.63252675 9.41400000 ;go bond 0.7099872721863867 +molecule_0_84 molecule_0_43 1 0.89270990 9.41400000 ;go bond 1.0020329775751635 +molecule_0_84 molecule_0_53 1 0.66502200 9.41400000 ;go bond 0.7464619538686407 +molecule_0_84 molecule_0_54 1 0.56665258 9.41400000 ;go bond 0.6360460147186728 +molecule_0_85 molecule_0_40 1 0.48170210 9.41400000 ;go bond 0.5406923273735796 +molecule_0_85 molecule_0_81 1 0.64785523 9.41400000 ;go bond 0.7271929039256984 +molecule_0_86 molecule_0_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 +molecule_0_86 molecule_0_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 +molecule_0_86 molecule_0_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 +molecule_0_88 molecule_0_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 +molecule_0_88 molecule_0_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 +molecule_0_88 molecule_0_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 +molecule_0_88 molecule_0_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 +molecule_0_88 molecule_0_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 +molecule_0_88 molecule_0_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 +molecule_0_89 molecule_0_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 +molecule_0_89 molecule_0_15 1 0.69215886 9.41400000 ;go bond 0.7769220558398894 +molecule_0_90 molecule_0_78 1 0.80563795 9.41400000 ;go bond 0.9042980239792853 +molecule_0_90 molecule_0_82 1 0.59740893 9.41400000 ;go bond 0.6705688513824994 +molecule_0_90 molecule_0_83 1 0.57714934 9.41400000 ;go bond 0.6478282257424317 +molecule_0_91 molecule_0_55 1 0.70847337 9.41400000 ;go bond 0.7952344695348353 +molecule_0_91 molecule_0_58 1 0.76773720 9.41400000 ;go bond 0.8617558647944001 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1 0.76727508 9.41400000 ;go bond 0.8612371596953154 +molecule_0_95 molecule_0_58 1 0.83998475 9.41400000 ;go bond 0.9428510053550558 +molecule_0_95 molecule_0_91 1 0.53148309 9.41400000 ;go bond 0.5965695928114466 +molecule_0_96 molecule_0_15 1 0.94537258 9.41400000 ;go bond 1.0611448446580265 +molecule_0_96 molecule_0_16 1 0.84805127 9.41400000 ;go bond 0.9519053644995195 +molecule_0_96 molecule_0_17 1 0.81454872 9.41400000 ;go bond 0.9143000281459933 +molecule_0_96 molecule_0_20 1 0.73587759 9.41400000 ;go bond 0.8259946673768416 +molecule_0_96 molecule_0_92 1 0.54860993 9.41400000 ;go bond 0.6157938252917854 +molecule_0_97 molecule_0_63 1 0.84557275 9.41400000 ;go bond 0.9491233248865086 +molecule_0_97 molecule_0_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 +molecule_0_97 molecule_0_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 +molecule_0_98 molecule_0_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 +molecule_0_98 molecule_0_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 +molecule_0_98 molecule_0_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 +molecule_0_99 molecule_0_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 +molecule_0_99 molecule_0_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 +molecule_0_99 molecule_0_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 +molecule_0_99 molecule_0_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 +molecule_0_100 molecule_0_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 +molecule_0_100 molecule_0_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 +molecule_0_100 molecule_0_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 +molecule_0_101 molecule_0_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 +molecule_0_104 molecule_0_23 1 0.90496194 9.41400000 ;go bond 1.0157854279713863 +molecule_0_104 molecule_0_99 1 0.37779975 9.41400000 ;go bond 0.42406587714866395 +molecule_0_105 molecule_0_23 1 0.85792539 9.41400000 ;go bond 0.9629886926477136 +molecule_0_105 molecule_0_27 1 0.80028132 9.41400000 ;go bond 0.8982854095190085 +molecule_0_105 molecule_0_28 1 0.85914649 9.41400000 ;go bond 0.9643593287596212 +molecule_0_105 molecule_0_31 1 0.84674626 9.41400000 ;go bond 0.950440544780807 +molecule_0_105 molecule_0_99 1 0.58741430 9.41400000 ;go bond 0.6593502594081683 +molecule_0_107 molecule_0_98 1 0.70183885 9.41400000 ;go bond 0.7877874714268905 +molecule_0_108 molecule_0_28 1 0.92956079 9.41400000 ;go bond 1.0433967044744268 +molecule_0_108 molecule_0_35 1 0.82960839 9.41400000 ;go bond 0.9312039368635526 +molecule_0_108 molecule_0_56 1 0.78133210 9.41400000 ;go bond 0.8770156294387439 +molecule_0_108 molecule_0_57 1 0.77168204 9.41400000 ;go bond 0.8661838041857776 +molecule_0_108 molecule_0_98 1 0.90403083 9.41400000 ;go bond 1.014740292066367 +molecule_0_108 molecule_0_99 1 0.90315750 9.41400000 ;go bond 1.0137600206889819 +molecule_0_110 molecule_0_34 1 0.54869664 9.41400000 ;go bond 0.6158911542488904 +molecule_0_110 molecule_0_35 1 0.64980269 9.41400000 ;go bond 0.7293788607697123 +molecule_0_111 molecule_0_27 1 0.70311941 9.41400000 ;go bond 0.7892248529963473 +molecule_0_111 molecule_0_31 1 0.56259884 9.41400000 ;go bond 0.6314958500157425 +molecule_0_111 molecule_0_105 1 0.59346888 9.41400000 ;go bond 0.6661462995266982 +molecule_0_111 molecule_0_106 1 0.59882239 9.41400000 ;go bond 0.6721554100763635 +molecule_0_112 molecule_0_106 1 0.57753815 9.41400000 ;go bond 0.6482646568405853 +molecule_0_112 molecule_0_107 1 0.74260248 9.41400000 ;go bond 0.833543103918769 +molecule_0_112 molecule_0_108 1 0.53753958 9.41400000 ;go bond 0.603367775987529 +molecule_0_113 molecule_0_109 1 0.53306219 9.41400000 ;go bond 0.5983420831461288 +molecule_0_114 molecule_0_34 1 0.72771145 9.41400000 ;go bond 0.8168284821715603 +molecule_0_114 molecule_0_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 +molecule_0_115 molecule_0_30 1 0.62277169 9.41400000 ;go bond 0.6990375917289473 +molecule_0_115 molecule_0_31 1 0.71820218 9.41400000 ;go bond 0.8061546928175227 +molecule_0_115 molecule_0_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 +molecule_0_115 molecule_0_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 +molecule_0_115 molecule_0_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 +molecule_0_116 molecule_0_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 +molecule_0_116 molecule_0_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 +molecule_0_116 molecule_0_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 +molecule_0_118 molecule_0_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 +molecule_0_120 molecule_0_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 +molecule_0_120 molecule_0_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 +molecule_0_120 molecule_0_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 +molecule_0_120 molecule_0_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 +molecule_0_120 molecule_0_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 +molecule_0_122 molecule_0_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 +molecule_0_123 molecule_0_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 +molecule_0_123 molecule_0_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 +molecule_0_123 molecule_0_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 +molecule_0_123 molecule_0_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 +molecule_0_123 molecule_0_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 +molecule_0_123 molecule_0_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 +molecule_0_124 molecule_0_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 +molecule_0_124 molecule_0_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 +molecule_0_124 molecule_0_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 +molecule_0_124 molecule_0_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 +molecule_0_124 molecule_0_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 +molecule_0_125 molecule_0_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 +molecule_0_125 molecule_0_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 +molecule_0_127 molecule_0_5 1 0.79805432 9.41400000 ;go bond 0.8957856911439042 +molecule_0_127 molecule_0_6 1 0.59870073 9.41400000 ;go bond 0.6720188457372778 +molecule_0_129 molecule_0_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 +molecule_0_129 molecule_0_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 +molecule_0_129 molecule_0_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 +molecule_0_129 molecule_0_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp similarity index 51% rename from vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule.itp rename to vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp index 70fa5fa0b..501335e6f 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule.itp +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp @@ -1,451 +1,450 @@ ; This file was generated using the following command: -; /coarse/chris/python_packages/vermouth_dev/vermouth-martinize/venv/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go ../map.map -noscfix -cys none -; martinize with vermouth 0.0.1.dev1783 +; /local/lborge01/martinize_stuff/dev_go/devmartinize/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go -go-map ../map.map +; martinize with vermouth 0.9.7.dev79 ; The following sequence of secondary structure ; was used for the full system: ; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -; Please cite the following papers: +; Pleas cite the following papers: ; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 -; Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; 2024; 10.1101/2024.04.15.589479 [ moleculetype ] -molecule 1 +molecule_0 1 [ atoms ] - 1 Q5 1 LYS BB 1 1 - 2 SC3 1 LYS SC1 2 0.0 - 3 SQ4p 1 LYS SC2 3 1.0 - 4 SP2 2 VAL BB 4 0.0 - 5 SC3 2 VAL SC1 5 0.0 - 6 P2 3 PHE BB 6 0.0 - 7 SC4 3 PHE SC1 7 0.0 - 8 TC5 3 PHE SC2 8 0.0 - 9 TC5 3 PHE SC3 9 0.0 - 10 SP1 4 GLY BB 10 0.0 - 11 P2 5 ARG BB 11 0.0 - 12 SC3 5 ARG SC1 12 0.0 - 13 SQ3p 5 ARG SC2 13 1.0 - 14 P2 6 CYS BB 14 0.0 - 15 TC6 6 CYS SC1 15 0.0 - 16 P2 7 GLU BB 16 0.0 - 17 Q5n 7 GLU SC1 17 -1.0 - 18 P2 8 LEU BB 18 0.0 - 19 SC2 8 LEU SC1 19 0.0 - 20 SP2 9 ALA BB 20 0.0 - 21 TC3 9 ALA SC1 21 0.0 - 22 SP2 10 ALA BB 22 0.0 - 23 TC3 10 ALA SC1 23 0.0 - 24 SP2 11 ALA BB 24 0.0 - 25 TC3 11 ALA SC1 25 0.0 - 26 P2 12 MET BB 26 0.0 - 27 C6 12 MET SC1 27 0.0 - 28 P2 13 LYS BB 28 0.0 - 29 SC3 13 LYS SC1 29 0.0 - 30 SQ4p 13 LYS SC2 30 1.0 - 31 P2 14 ARG BB 31 0.0 - 32 SC3 14 ARG SC1 32 0.0 - 33 SQ3p 14 ARG SC2 33 1.0 - 34 P2 15 HIS BB 34 0.0 - 35 TC4 15 HIS SC1 35 0.0 - 36 TN6d 15 HIS SC2 36 0.0 - 37 TN5a 15 HIS SC3 37 0.0 - 38 SP1 16 GLY BB 38 0.0 - 39 P2 17 LEU BB 39 0.0 - 40 SC2 17 LEU SC1 40 0.0 - 41 P2 18 ASP BB 41 0.0 - 42 SQ5n 18 ASP SC1 42 -1.0 - 43 P2 19 ASN BB 43 0.0 - 44 SP5 19 ASN SC1 44 0.0 - 45 P2 20 TYR BB 45 0.0 - 46 TC4 20 TYR SC1 46 0.0 - 47 TC5 20 TYR SC2 47 0.0 - 48 TC5 20 TYR SC3 48 0.0 - 49 TN6 20 TYR SC4 49 0.0 - 50 P2 21 ARG BB 50 0.0 - 51 SC3 21 ARG SC1 51 0.0 - 52 SQ3p 21 ARG SC2 52 1.0 - 53 SP1 22 GLY BB 53 0.0 - 54 P2 23 TYR BB 54 0.0 - 55 TC4 23 TYR SC1 55 0.0 - 56 TC5 23 TYR SC2 56 0.0 - 57 TC5 23 TYR SC3 57 0.0 - 58 TN6 23 TYR SC4 58 0.0 - 59 P2 24 SER BB 59 0.0 - 60 TP1 24 SER SC1 60 0.0 - 61 P2 25 LEU BB 61 0.0 - 62 SC2 25 LEU SC1 62 0.0 - 63 SP1 26 GLY BB 63 0.0 - 64 P2 27 ASN BB 64 0.0 - 65 SP5 27 ASN SC1 65 0.0 - 66 P2 28 TRP BB 66 0.0 - 67 TC4 28 TRP SC1 67 0.0 36.0 - 68 TN6d 28 TRP SC2 68 0.0 36.0 - 69 TC5 28 TRP SC3 69 0.0 0.0 - 70 TC5 28 TRP SC4 70 0.0 36.0 - 71 TC5 28 TRP SC5 71 0.0 36.0 - 72 SP2 29 VAL BB 72 0.0 - 73 SC3 29 VAL SC1 73 0.0 - 74 P2 30 CYS BB 74 0.0 - 75 TC6 30 CYS SC1 75 0.0 - 76 SP2 31 ALA BB 76 0.0 - 77 TC3 31 ALA SC1 77 0.0 - 78 SP2 32 ALA BB 78 0.0 - 79 TC3 32 ALA SC1 79 0.0 - 80 P2 33 LYS BB 80 0.0 - 81 SC3 33 LYS SC1 81 0.0 - 82 SQ4p 33 LYS SC2 82 1.0 - 83 P2 34 PHE BB 83 0.0 - 84 SC4 34 PHE SC1 84 0.0 - 85 TC5 34 PHE SC2 85 0.0 - 86 TC5 34 PHE SC3 86 0.0 - 87 P2 35 GLU BB 87 0.0 - 88 Q5n 35 GLU SC1 88 -1.0 - 89 P2 36 SER BB 89 0.0 - 90 TP1 36 SER SC1 90 0.0 - 91 P2 37 ASN BB 91 0.0 - 92 SP5 37 ASN SC1 92 0.0 - 93 P2 38 PHE BB 93 0.0 - 94 SC4 38 PHE SC1 94 0.0 - 95 TC5 38 PHE SC2 95 0.0 - 96 TC5 38 PHE SC3 96 0.0 - 97 P2 39 ASN BB 97 0.0 - 98 SP5 39 ASN SC1 98 0.0 - 99 P2 40 THR BB 99 0.0 -100 SP1 40 THR SC1 100 0.0 -101 P2 41 GLN BB 101 0.0 -102 P5 41 GLN SC1 102 0.0 -103 SP2 42 ALA BB 103 0.0 -104 TC3 42 ALA SC1 104 0.0 -105 P2 43 THR BB 105 0.0 -106 SP1 43 THR SC1 106 0.0 -107 P2 44 ASN BB 107 0.0 -108 SP5 44 ASN SC1 108 0.0 -109 P2 45 ARG BB 109 0.0 -110 SC3 45 ARG SC1 110 0.0 -111 SQ3p 45 ARG SC2 111 1.0 -112 P2 46 ASN BB 112 0.0 -113 SP5 46 ASN SC1 113 0.0 -114 P2 47 THR BB 114 0.0 -115 SP1 47 THR SC1 115 0.0 -116 P2 48 ASP BB 116 0.0 -117 SQ5n 48 ASP SC1 117 -1.0 -118 SP1 49 GLY BB 118 0.0 -119 P2 50 SER BB 119 0.0 -120 TP1 50 SER SC1 120 0.0 -121 P2 51 THR BB 121 0.0 -122 SP1 51 THR SC1 122 0.0 -123 P2 52 ASP BB 123 0.0 -124 SQ5n 52 ASP SC1 124 -1.0 -125 P2 53 TYR BB 125 0.0 -126 TC4 53 TYR SC1 126 0.0 -127 TC5 53 TYR SC2 127 0.0 -128 TC5 53 TYR SC3 128 0.0 -129 TN6 53 TYR SC4 129 0.0 -130 SP1 54 GLY BB 130 0.0 -131 P2 55 ILE BB 131 0.0 -132 SC2 55 ILE SC1 132 0.0 -133 P2 56 LEU BB 133 0.0 -134 SC2 56 LEU SC1 134 0.0 -135 P2 57 GLN BB 135 0.0 -136 P5 57 GLN SC1 136 0.0 -137 P2 58 ILE BB 137 0.0 -138 SC2 58 ILE SC1 138 0.0 -139 P2 59 ASN BB 139 0.0 -140 SP5 59 ASN SC1 140 0.0 -141 P2 60 SER BB 141 0.0 -142 TP1 60 SER SC1 142 0.0 -143 P2 61 ARG BB 143 0.0 -144 SC3 61 ARG SC1 144 0.0 -145 SQ3p 61 ARG SC2 145 1.0 -146 P2 62 TRP BB 146 0.0 -147 TC4 62 TRP SC1 147 0.0 36.0 -148 TN6d 62 TRP SC2 148 0.0 36.0 -149 TC5 62 TRP SC3 149 0.0 0.0 -150 TC5 62 TRP SC4 150 0.0 36.0 -151 TC5 62 TRP SC5 151 0.0 36.0 -152 P2 63 TRP BB 152 0.0 -153 TC4 63 TRP SC1 153 0.0 36.0 -154 TN6d 63 TRP SC2 154 0.0 36.0 -155 TC5 63 TRP SC3 155 0.0 0.0 -156 TC5 63 TRP SC4 156 0.0 36.0 -157 TC5 63 TRP SC5 157 0.0 36.0 -158 P2 64 CYS BB 158 0.0 -159 TC6 64 CYS SC1 159 0.0 -160 P2 65 ASN BB 160 0.0 -161 SP5 65 ASN SC1 161 0.0 -162 P2 66 ASP BB 162 0.0 -163 SQ5n 66 ASP SC1 163 -1.0 -164 SP1 67 GLY BB 164 0.0 -165 P2 68 ARG BB 165 0.0 -166 SC3 68 ARG SC1 166 0.0 -167 SQ3p 68 ARG SC2 167 1.0 -168 P2 69 THR BB 168 0.0 -169 SP1 69 THR SC1 169 0.0 -170 SP2a 70 PRO BB 170 0.0 -171 SC3 70 PRO SC1 171 0.0 -172 SP1 71 GLY BB 172 0.0 -173 P2 72 SER BB 173 0.0 -174 TP1 72 SER SC1 174 0.0 -175 P2 73 ARG BB 175 0.0 -176 SC3 73 ARG SC1 176 0.0 -177 SQ3p 73 ARG SC2 177 1.0 -178 P2 74 ASN BB 178 0.0 -179 SP5 74 ASN SC1 179 0.0 -180 P2 75 LEU BB 180 0.0 -181 SC2 75 LEU SC1 181 0.0 -182 P2 76 CYS BB 182 0.0 -183 TC6 76 CYS SC1 183 0.0 -184 P2 77 ASN BB 184 0.0 -185 SP5 77 ASN SC1 185 0.0 -186 P2 78 ILE BB 186 0.0 -187 SC2 78 ILE SC1 187 0.0 -188 SP2a 79 PRO BB 188 0.0 -189 SC3 79 PRO SC1 189 0.0 -190 P2 80 CYS BB 190 0.0 -191 TC6 80 CYS SC1 191 0.0 -192 P2 81 SER BB 192 0.0 -193 TP1 81 SER SC1 193 0.0 -194 SP2 82 ALA BB 194 0.0 -195 TC3 82 ALA SC1 195 0.0 -196 P2 83 LEU BB 196 0.0 -197 SC2 83 LEU SC1 197 0.0 -198 P2 84 LEU BB 198 0.0 -199 SC2 84 LEU SC1 199 0.0 -200 P2 85 SER BB 200 0.0 -201 TP1 85 SER SC1 201 0.0 -202 P2 86 SER BB 202 0.0 -203 TP1 86 SER SC1 203 0.0 -204 P2 87 ASP BB 204 0.0 -205 SQ5n 87 ASP SC1 205 -1.0 -206 P2 88 ILE BB 206 0.0 -207 SC2 88 ILE SC1 207 0.0 -208 P2 89 THR BB 208 0.0 -209 SP1 89 THR SC1 209 0.0 -210 SP2 90 ALA BB 210 0.0 -211 TC3 90 ALA SC1 211 0.0 -212 P2 91 SER BB 212 0.0 -213 TP1 91 SER SC1 213 0.0 -214 SP2 92 VAL BB 214 0.0 -215 SC3 92 VAL SC1 215 0.0 -216 P2 93 ASN BB 216 0.0 -217 SP5 93 ASN SC1 217 0.0 -218 P2 94 CYS BB 218 0.0 -219 TC6 94 CYS SC1 219 0.0 -220 SP2 95 ALA BB 220 0.0 -221 TC3 95 ALA SC1 221 0.0 -222 P2 96 LYS BB 222 0.0 -223 SC3 96 LYS SC1 223 0.0 -224 SQ4p 96 LYS SC2 224 1.0 -225 P2 97 LYS BB 225 0.0 -226 SC3 97 LYS SC1 226 0.0 -227 SQ4p 97 LYS SC2 227 1.0 -228 P2 98 ILE BB 228 0.0 -229 SC2 98 ILE SC1 229 0.0 -230 SP2 99 VAL BB 230 0.0 -231 SC3 99 VAL SC1 231 0.0 -232 P2 100 SER BB 232 0.0 -233 TP1 100 SER SC1 233 0.0 -234 P2 101 ASP BB 234 0.0 -235 SQ5n 101 ASP SC1 235 -1.0 -236 SP1 102 GLY BB 236 0.0 -237 P2 103 ASN BB 237 0.0 -238 SP5 103 ASN SC1 238 0.0 -239 SP1 104 GLY BB 239 0.0 -240 P2 105 MET BB 240 0.0 -241 C6 105 MET SC1 241 0.0 -242 P2 106 ASN BB 242 0.0 -243 SP5 106 ASN SC1 243 0.0 -244 SP2 107 ALA BB 244 0.0 -245 TC3 107 ALA SC1 245 0.0 -246 P2 108 TRP BB 246 0.0 -247 TC4 108 TRP SC1 247 0.0 36.0 -248 TN6d 108 TRP SC2 248 0.0 36.0 -249 TC5 108 TRP SC3 249 0.0 0.0 -250 TC5 108 TRP SC4 250 0.0 36.0 -251 TC5 108 TRP SC5 251 0.0 36.0 -252 SP2 109 VAL BB 252 0.0 -253 SC3 109 VAL SC1 253 0.0 -254 SP2 110 ALA BB 254 0.0 -255 TC3 110 ALA SC1 255 0.0 -256 P2 111 TRP BB 256 0.0 -257 TC4 111 TRP SC1 257 0.0 36.0 -258 TN6d 111 TRP SC2 258 0.0 36.0 -259 TC5 111 TRP SC3 259 0.0 0.0 -260 TC5 111 TRP SC4 260 0.0 36.0 -261 TC5 111 TRP SC5 261 0.0 36.0 -262 P2 112 ARG BB 262 0.0 -263 SC3 112 ARG SC1 263 0.0 -264 SQ3p 112 ARG SC2 264 1.0 -265 P2 113 ASN BB 265 0.0 -266 SP5 113 ASN SC1 266 0.0 -267 P2 114 ARG BB 267 0.0 -268 SC3 114 ARG SC1 268 0.0 -269 SQ3p 114 ARG SC2 269 1.0 -270 P2 115 CYS BB 270 0.0 -271 TC6 115 CYS SC1 271 0.0 -272 P2 116 LYS BB 272 0.0 -273 SC3 116 LYS SC1 273 0.0 -274 SQ4p 116 LYS SC2 274 1.0 -275 SP1 117 GLY BB 275 0.0 -276 P2 118 THR BB 276 0.0 -277 SP1 118 THR SC1 277 0.0 -278 P2 119 ASP BB 278 0.0 -279 SQ5n 119 ASP SC1 279 -1.0 -280 SP2 120 VAL BB 280 0.0 -281 SC3 120 VAL SC1 281 0.0 -282 P2 121 GLN BB 282 0.0 -283 P5 121 GLN SC1 283 0.0 -284 SP2 122 ALA BB 284 0.0 -285 TC3 122 ALA SC1 285 0.0 -286 P2 123 TRP BB 286 0.0 -287 TC4 123 TRP SC1 287 0.0 36.0 -288 TN6d 123 TRP SC2 288 0.0 36.0 -289 TC5 123 TRP SC3 289 0.0 0.0 -290 TC5 123 TRP SC4 290 0.0 36.0 -291 TC5 123 TRP SC5 291 0.0 36.0 -292 P2 124 ILE BB 292 0.0 -293 SC2 124 ILE SC1 293 0.0 -294 P2 125 ARG BB 294 0.0 -295 SC3 125 ARG SC1 295 0.0 -296 SQ3p 125 ARG SC2 296 1.0 -297 SP1 126 GLY BB 297 0.0 -298 P2 127 CYS BB 298 0.0 -299 TC6 127 CYS SC1 299 0.0 -300 P2 128 ARG BB 300 0.0 -301 SC3 128 ARG SC1 301 0.0 -302 SQ3p 128 ARG SC2 302 1.0 -303 Q5 129 LEU BB 303 -1 -304 SC2 129 LEU SC1 304 0.0 -305 molecule_1 1 LYS CA 305 0 0.0 -306 molecule_2 2 VAL CA 306 0 0.0 -307 molecule_3 3 PHE CA 307 0 0.0 -308 molecule_4 4 GLY CA 308 0 0.0 -309 molecule_5 5 ARG CA 309 0 0.0 -310 molecule_6 6 CYS CA 310 0 0.0 -311 molecule_7 7 GLU CA 311 0 0.0 -312 molecule_8 8 LEU CA 312 0 0.0 -313 molecule_9 9 ALA CA 313 0 0.0 -314 molecule_10 10 ALA CA 314 0 0.0 -315 molecule_11 11 ALA CA 315 0 0.0 -316 molecule_12 12 MET CA 316 0 0.0 -317 molecule_13 13 LYS CA 317 0 0.0 -318 molecule_14 14 ARG CA 318 0 0.0 -319 molecule_15 15 HIS CA 319 0 0.0 -320 molecule_16 16 GLY CA 320 0 0.0 -321 molecule_17 17 LEU CA 321 0 0.0 -322 molecule_18 18 ASP CA 322 0 0.0 -323 molecule_19 19 ASN CA 323 0 0.0 -324 molecule_20 20 TYR CA 324 0 0.0 -325 molecule_21 21 ARG CA 325 0 0.0 -326 molecule_22 22 GLY CA 326 0 0.0 -327 molecule_23 23 TYR CA 327 0 0.0 -328 molecule_24 24 SER CA 328 0 0.0 -329 molecule_25 25 LEU CA 329 0 0.0 -330 molecule_26 26 GLY CA 330 0 0.0 -331 molecule_27 27 ASN CA 331 0 0.0 -332 molecule_28 28 TRP CA 332 0 0.0 -333 molecule_29 29 VAL CA 333 0 0.0 -334 molecule_30 30 CYS CA 334 0 0.0 -335 molecule_31 31 ALA CA 335 0 0.0 -336 molecule_32 32 ALA CA 336 0 0.0 -337 molecule_33 33 LYS CA 337 0 0.0 -338 molecule_34 34 PHE CA 338 0 0.0 -339 molecule_35 35 GLU CA 339 0 0.0 -340 molecule_36 36 SER CA 340 0 0.0 -341 molecule_37 37 ASN CA 341 0 0.0 -342 molecule_38 38 PHE CA 342 0 0.0 -343 molecule_39 39 ASN CA 343 0 0.0 -344 molecule_40 40 THR CA 344 0 0.0 -345 molecule_41 41 GLN CA 345 0 0.0 -346 molecule_42 42 ALA CA 346 0 0.0 -347 molecule_43 43 THR CA 347 0 0.0 -348 molecule_44 44 ASN CA 348 0 0.0 -349 molecule_45 45 ARG CA 349 0 0.0 -350 molecule_46 46 ASN CA 350 0 0.0 -351 molecule_47 47 THR CA 351 0 0.0 -352 molecule_48 48 ASP CA 352 0 0.0 -353 molecule_49 49 GLY CA 353 0 0.0 -354 molecule_50 50 SER CA 354 0 0.0 -355 molecule_51 51 THR CA 355 0 0.0 -356 molecule_52 52 ASP CA 356 0 0.0 -357 molecule_53 53 TYR CA 357 0 0.0 -358 molecule_54 54 GLY CA 358 0 0.0 -359 molecule_55 55 ILE CA 359 0 0.0 -360 molecule_56 56 LEU CA 360 0 0.0 -361 molecule_57 57 GLN CA 361 0 0.0 -362 molecule_58 58 ILE CA 362 0 0.0 -363 molecule_59 59 ASN CA 363 0 0.0 -364 molecule_60 60 SER CA 364 0 0.0 -365 molecule_61 61 ARG CA 365 0 0.0 -366 molecule_62 62 TRP CA 366 0 0.0 -367 molecule_63 63 TRP CA 367 0 0.0 -368 molecule_64 64 CYS CA 368 0 0.0 -369 molecule_65 65 ASN CA 369 0 0.0 -370 molecule_66 66 ASP CA 370 0 0.0 -371 molecule_67 67 GLY CA 371 0 0.0 -372 molecule_68 68 ARG CA 372 0 0.0 -373 molecule_69 69 THR CA 373 0 0.0 -374 molecule_70 70 PRO CA 374 0 0.0 -375 molecule_71 71 GLY CA 375 0 0.0 -376 molecule_72 72 SER CA 376 0 0.0 -377 molecule_73 73 ARG CA 377 0 0.0 -378 molecule_74 74 ASN CA 378 0 0.0 -379 molecule_75 75 LEU CA 379 0 0.0 -380 molecule_76 76 CYS CA 380 0 0.0 -381 molecule_77 77 ASN CA 381 0 0.0 -382 molecule_78 78 ILE CA 382 0 0.0 -383 molecule_79 79 PRO CA 383 0 0.0 -384 molecule_80 80 CYS CA 384 0 0.0 -385 molecule_81 81 SER CA 385 0 0.0 -386 molecule_82 82 ALA CA 386 0 0.0 -387 molecule_83 83 LEU CA 387 0 0.0 -388 molecule_84 84 LEU CA 388 0 0.0 -389 molecule_85 85 SER CA 389 0 0.0 -390 molecule_86 86 SER CA 390 0 0.0 -391 molecule_87 87 ASP CA 391 0 0.0 -392 molecule_88 88 ILE CA 392 0 0.0 -393 molecule_89 89 THR CA 393 0 0.0 -394 molecule_90 90 ALA CA 394 0 0.0 -395 molecule_91 91 SER CA 395 0 0.0 -396 molecule_92 92 VAL CA 396 0 0.0 -397 molecule_93 93 ASN CA 397 0 0.0 -398 molecule_94 94 CYS CA 398 0 0.0 -399 molecule_95 95 ALA CA 399 0 0.0 -400 molecule_96 96 LYS CA 400 0 0.0 -401 molecule_97 97 LYS CA 401 0 0.0 -402 molecule_98 98 ILE CA 402 0 0.0 -403 molecule_99 99 VAL CA 403 0 0.0 -404 molecule_100 100 SER CA 404 0 0.0 -405 molecule_101 101 ASP CA 405 0 0.0 -406 molecule_102 102 GLY CA 406 0 0.0 -407 molecule_103 103 ASN CA 407 0 0.0 -408 molecule_104 104 GLY CA 408 0 0.0 -409 molecule_105 105 MET CA 409 0 0.0 -410 molecule_106 106 ASN CA 410 0 0.0 -411 molecule_107 107 ALA CA 411 0 0.0 -412 molecule_108 108 TRP CA 412 0 0.0 -413 molecule_109 109 VAL CA 413 0 0.0 -414 molecule_110 110 ALA CA 414 0 0.0 -415 molecule_111 111 TRP CA 415 0 0.0 -416 molecule_112 112 ARG CA 416 0 0.0 -417 molecule_113 113 ASN CA 417 0 0.0 -418 molecule_114 114 ARG CA 418 0 0.0 -419 molecule_115 115 CYS CA 419 0 0.0 -420 molecule_116 116 LYS CA 420 0 0.0 -421 molecule_117 117 GLY CA 421 0 0.0 -422 molecule_118 118 THR CA 422 0 0.0 -423 molecule_119 119 ASP CA 423 0 0.0 -424 molecule_120 120 VAL CA 424 0 0.0 -425 molecule_121 121 GLN CA 425 0 0.0 -426 molecule_122 122 ALA CA 426 0 0.0 -427 molecule_123 123 TRP CA 427 0 0.0 -428 molecule_124 124 ILE CA 428 0 0.0 -429 molecule_125 125 ARG CA 429 0 0.0 -430 molecule_126 126 GLY CA 430 0 0.0 -431 molecule_127 127 CYS CA 431 0 0.0 -432 molecule_128 128 ARG CA 432 0 0.0 -433 molecule_129 129 LEU CA 433 0 0.0 + 1 Q5 1 LYS BB 1 1 + 2 SC3 1 LYS SC1 2 0.0 + 3 SQ4p 1 LYS SC2 3 1.0 + 4 SP2 2 VAL BB 4 0.0 + 5 SC3 2 VAL SC1 5 0.0 + 6 P2 3 PHE BB 6 0.0 + 7 SC4 3 PHE SC1 7 0.0 + 8 TC5 3 PHE SC2 8 0.0 + 9 TC5 3 PHE SC3 9 0.0 + 10 SP1 4 GLY BB 10 0.0 + 11 P2 5 ARG BB 11 0.0 + 12 SC3 5 ARG SC1 12 0.0 + 13 SQ3p 5 ARG SC2 13 1.0 + 14 P2 6 CYS BB 14 0.0 + 15 TC6 6 CYS SC1 15 0.0 + 16 P2 7 GLU BB 16 0.0 + 17 Q5n 7 GLU SC1 17 -1.0 + 18 P2 8 LEU BB 18 0.0 + 19 SC2 8 LEU SC1 19 0.0 + 20 SP2 9 ALA BB 20 0.0 + 21 TC3 9 ALA SC1 21 0.0 + 22 SP2 10 ALA BB 22 0.0 + 23 TC3 10 ALA SC1 23 0.0 + 24 SP2 11 ALA BB 24 0.0 + 25 TC3 11 ALA SC1 25 0.0 + 26 P2 12 MET BB 26 0.0 + 27 C6 12 MET SC1 27 0.0 + 28 P2 13 LYS BB 28 0.0 + 29 SC3 13 LYS SC1 29 0.0 + 30 SQ4p 13 LYS SC2 30 1.0 + 31 P2 14 ARG BB 31 0.0 + 32 SC3 14 ARG SC1 32 0.0 + 33 SQ3p 14 ARG SC2 33 1.0 + 34 P2 15 HIS BB 34 0.0 + 35 TC4 15 HIS SC1 35 0.0 + 36 TN6d 15 HIS SC2 36 0.0 + 37 TN5a 15 HIS SC3 37 0.0 + 38 SP1 16 GLY BB 38 0.0 + 39 P2 17 LEU BB 39 0.0 + 40 SC2 17 LEU SC1 40 0.0 + 41 P2 18 ASP BB 41 0.0 + 42 SQ5n 18 ASP SC1 42 -1.0 + 43 P2 19 ASN BB 43 0.0 + 44 SP5 19 ASN SC1 44 0.0 + 45 P2 20 TYR BB 45 0.0 + 46 TC4 20 TYR SC1 46 0.0 + 47 TC5 20 TYR SC2 47 0.0 + 48 TC5 20 TYR SC3 48 0.0 + 49 TN6 20 TYR SC4 49 0.0 + 50 P2 21 ARG BB 50 0.0 + 51 SC3 21 ARG SC1 51 0.0 + 52 SQ3p 21 ARG SC2 52 1.0 + 53 SP1 22 GLY BB 53 0.0 + 54 P2 23 TYR BB 54 0.0 + 55 TC4 23 TYR SC1 55 0.0 + 56 TC5 23 TYR SC2 56 0.0 + 57 TC5 23 TYR SC3 57 0.0 + 58 TN6 23 TYR SC4 58 0.0 + 59 P2 24 SER BB 59 0.0 + 60 TP1 24 SER SC1 60 0.0 + 61 P2 25 LEU BB 61 0.0 + 62 SC2 25 LEU SC1 62 0.0 + 63 SP1 26 GLY BB 63 0.0 + 64 P2 27 ASN BB 64 0.0 + 65 SP5 27 ASN SC1 65 0.0 + 66 P2 28 TRP BB 66 0.0 + 67 TC4 28 TRP SC1 67 0.0 36.0 + 68 TN6d 28 TRP SC2 68 0.0 36.0 + 69 TC5 28 TRP SC3 69 0.0 0.0 + 70 TC5 28 TRP SC4 70 0.0 36.0 + 71 TC5 28 TRP SC5 71 0.0 36.0 + 72 SP2 29 VAL BB 72 0.0 + 73 SC3 29 VAL SC1 73 0.0 + 74 P2 30 CYS BB 74 0.0 + 75 TC6 30 CYS SC1 75 0.0 + 76 SP2 31 ALA BB 76 0.0 + 77 TC3 31 ALA SC1 77 0.0 + 78 SP2 32 ALA BB 78 0.0 + 79 TC3 32 ALA SC1 79 0.0 + 80 P2 33 LYS BB 80 0.0 + 81 SC3 33 LYS SC1 81 0.0 + 82 SQ4p 33 LYS SC2 82 1.0 + 83 P2 34 PHE BB 83 0.0 + 84 SC4 34 PHE SC1 84 0.0 + 85 TC5 34 PHE SC2 85 0.0 + 86 TC5 34 PHE SC3 86 0.0 + 87 P2 35 GLU BB 87 0.0 + 88 Q5n 35 GLU SC1 88 -1.0 + 89 P2 36 SER BB 89 0.0 + 90 TP1 36 SER SC1 90 0.0 + 91 P2 37 ASN BB 91 0.0 + 92 SP5 37 ASN SC1 92 0.0 + 93 P2 38 PHE BB 93 0.0 + 94 SC4 38 PHE SC1 94 0.0 + 95 TC5 38 PHE SC2 95 0.0 + 96 TC5 38 PHE SC3 96 0.0 + 97 P2 39 ASN BB 97 0.0 + 98 SP5 39 ASN SC1 98 0.0 + 99 P2 40 THR BB 99 0.0 +100 SP1 40 THR SC1 100 0.0 +101 P2 41 GLN BB 101 0.0 +102 P5 41 GLN SC1 102 0.0 +103 SP2 42 ALA BB 103 0.0 +104 TC3 42 ALA SC1 104 0.0 +105 P2 43 THR BB 105 0.0 +106 SP1 43 THR SC1 106 0.0 +107 P2 44 ASN BB 107 0.0 +108 SP5 44 ASN SC1 108 0.0 +109 P2 45 ARG BB 109 0.0 +110 SC3 45 ARG SC1 110 0.0 +111 SQ3p 45 ARG SC2 111 1.0 +112 P2 46 ASN BB 112 0.0 +113 SP5 46 ASN SC1 113 0.0 +114 P2 47 THR BB 114 0.0 +115 SP1 47 THR SC1 115 0.0 +116 P2 48 ASP BB 116 0.0 +117 SQ5n 48 ASP SC1 117 -1.0 +118 SP1 49 GLY BB 118 0.0 +119 P2 50 SER BB 119 0.0 +120 TP1 50 SER SC1 120 0.0 +121 P2 51 THR BB 121 0.0 +122 SP1 51 THR SC1 122 0.0 +123 P2 52 ASP BB 123 0.0 +124 SQ5n 52 ASP SC1 124 -1.0 +125 P2 53 TYR BB 125 0.0 +126 TC4 53 TYR SC1 126 0.0 +127 TC5 53 TYR SC2 127 0.0 +128 TC5 53 TYR SC3 128 0.0 +129 TN6 53 TYR SC4 129 0.0 +130 SP1 54 GLY BB 130 0.0 +131 P2 55 ILE BB 131 0.0 +132 SC2 55 ILE SC1 132 0.0 +133 P2 56 LEU BB 133 0.0 +134 SC2 56 LEU SC1 134 0.0 +135 P2 57 GLN BB 135 0.0 +136 P5 57 GLN SC1 136 0.0 +137 P2 58 ILE BB 137 0.0 +138 SC2 58 ILE SC1 138 0.0 +139 P2 59 ASN BB 139 0.0 +140 SP5 59 ASN SC1 140 0.0 +141 P2 60 SER BB 141 0.0 +142 TP1 60 SER SC1 142 0.0 +143 P2 61 ARG BB 143 0.0 +144 SC3 61 ARG SC1 144 0.0 +145 SQ3p 61 ARG SC2 145 1.0 +146 P2 62 TRP BB 146 0.0 +147 TC4 62 TRP SC1 147 0.0 36.0 +148 TN6d 62 TRP SC2 148 0.0 36.0 +149 TC5 62 TRP SC3 149 0.0 0.0 +150 TC5 62 TRP SC4 150 0.0 36.0 +151 TC5 62 TRP SC5 151 0.0 36.0 +152 P2 63 TRP BB 152 0.0 +153 TC4 63 TRP SC1 153 0.0 36.0 +154 TN6d 63 TRP SC2 154 0.0 36.0 +155 TC5 63 TRP SC3 155 0.0 0.0 +156 TC5 63 TRP SC4 156 0.0 36.0 +157 TC5 63 TRP SC5 157 0.0 36.0 +158 P2 64 CYS BB 158 0.0 +159 TC6 64 CYS SC1 159 0.0 +160 P2 65 ASN BB 160 0.0 +161 SP5 65 ASN SC1 161 0.0 +162 P2 66 ASP BB 162 0.0 +163 SQ5n 66 ASP SC1 163 -1.0 +164 SP1 67 GLY BB 164 0.0 +165 P2 68 ARG BB 165 0.0 +166 SC3 68 ARG SC1 166 0.0 +167 SQ3p 68 ARG SC2 167 1.0 +168 P2 69 THR BB 168 0.0 +169 SP1 69 THR SC1 169 0.0 +170 SP2a 70 PRO BB 170 0.0 +171 SC3 70 PRO SC1 171 0.0 +172 SP1 71 GLY BB 172 0.0 +173 P2 72 SER BB 173 0.0 +174 TP1 72 SER SC1 174 0.0 +175 P2 73 ARG BB 175 0.0 +176 SC3 73 ARG SC1 176 0.0 +177 SQ3p 73 ARG SC2 177 1.0 +178 P2 74 ASN BB 178 0.0 +179 SP5 74 ASN SC1 179 0.0 +180 P2 75 LEU BB 180 0.0 +181 SC2 75 LEU SC1 181 0.0 +182 P2 76 CYS BB 182 0.0 +183 TC6 76 CYS SC1 183 0.0 +184 P2 77 ASN BB 184 0.0 +185 SP5 77 ASN SC1 185 0.0 +186 P2 78 ILE BB 186 0.0 +187 SC2 78 ILE SC1 187 0.0 +188 SP2a 79 PRO BB 188 0.0 +189 SC3 79 PRO SC1 189 0.0 +190 P2 80 CYS BB 190 0.0 +191 TC6 80 CYS SC1 191 0.0 +192 P2 81 SER BB 192 0.0 +193 TP1 81 SER SC1 193 0.0 +194 SP2 82 ALA BB 194 0.0 +195 TC3 82 ALA SC1 195 0.0 +196 P2 83 LEU BB 196 0.0 +197 SC2 83 LEU SC1 197 0.0 +198 P2 84 LEU BB 198 0.0 +199 SC2 84 LEU SC1 199 0.0 +200 P2 85 SER BB 200 0.0 +201 TP1 85 SER SC1 201 0.0 +202 P2 86 SER BB 202 0.0 +203 TP1 86 SER SC1 203 0.0 +204 P2 87 ASP BB 204 0.0 +205 SQ5n 87 ASP SC1 205 -1.0 +206 P2 88 ILE BB 206 0.0 +207 SC2 88 ILE SC1 207 0.0 +208 P2 89 THR BB 208 0.0 +209 SP1 89 THR SC1 209 0.0 +210 SP2 90 ALA BB 210 0.0 +211 TC3 90 ALA SC1 211 0.0 +212 P2 91 SER BB 212 0.0 +213 TP1 91 SER SC1 213 0.0 +214 SP2 92 VAL BB 214 0.0 +215 SC3 92 VAL SC1 215 0.0 +216 P2 93 ASN BB 216 0.0 +217 SP5 93 ASN SC1 217 0.0 +218 P2 94 CYS BB 218 0.0 +219 TC6 94 CYS SC1 219 0.0 +220 SP2 95 ALA BB 220 0.0 +221 TC3 95 ALA SC1 221 0.0 +222 P2 96 LYS BB 222 0.0 +223 SC3 96 LYS SC1 223 0.0 +224 SQ4p 96 LYS SC2 224 1.0 +225 P2 97 LYS BB 225 0.0 +226 SC3 97 LYS SC1 226 0.0 +227 SQ4p 97 LYS SC2 227 1.0 +228 P2 98 ILE BB 228 0.0 +229 SC2 98 ILE SC1 229 0.0 +230 SP2 99 VAL BB 230 0.0 +231 SC3 99 VAL SC1 231 0.0 +232 P2 100 SER BB 232 0.0 +233 TP1 100 SER SC1 233 0.0 +234 P2 101 ASP BB 234 0.0 +235 SQ5n 101 ASP SC1 235 -1.0 +236 SP1 102 GLY BB 236 0.0 +237 P2 103 ASN BB 237 0.0 +238 SP5 103 ASN SC1 238 0.0 +239 SP1 104 GLY BB 239 0.0 +240 P2 105 MET BB 240 0.0 +241 C6 105 MET SC1 241 0.0 +242 P2 106 ASN BB 242 0.0 +243 SP5 106 ASN SC1 243 0.0 +244 SP2 107 ALA BB 244 0.0 +245 TC3 107 ALA SC1 245 0.0 +246 P2 108 TRP BB 246 0.0 +247 TC4 108 TRP SC1 247 0.0 36.0 +248 TN6d 108 TRP SC2 248 0.0 36.0 +249 TC5 108 TRP SC3 249 0.0 0.0 +250 TC5 108 TRP SC4 250 0.0 36.0 +251 TC5 108 TRP SC5 251 0.0 36.0 +252 SP2 109 VAL BB 252 0.0 +253 SC3 109 VAL SC1 253 0.0 +254 SP2 110 ALA BB 254 0.0 +255 TC3 110 ALA SC1 255 0.0 +256 P2 111 TRP BB 256 0.0 +257 TC4 111 TRP SC1 257 0.0 36.0 +258 TN6d 111 TRP SC2 258 0.0 36.0 +259 TC5 111 TRP SC3 259 0.0 0.0 +260 TC5 111 TRP SC4 260 0.0 36.0 +261 TC5 111 TRP SC5 261 0.0 36.0 +262 P2 112 ARG BB 262 0.0 +263 SC3 112 ARG SC1 263 0.0 +264 SQ3p 112 ARG SC2 264 1.0 +265 P2 113 ASN BB 265 0.0 +266 SP5 113 ASN SC1 266 0.0 +267 P2 114 ARG BB 267 0.0 +268 SC3 114 ARG SC1 268 0.0 +269 SQ3p 114 ARG SC2 269 1.0 +270 P2 115 CYS BB 270 0.0 +271 TC6 115 CYS SC1 271 0.0 +272 P2 116 LYS BB 272 0.0 +273 SC3 116 LYS SC1 273 0.0 +274 SQ4p 116 LYS SC2 274 1.0 +275 SP1 117 GLY BB 275 0.0 +276 P2 118 THR BB 276 0.0 +277 SP1 118 THR SC1 277 0.0 +278 P2 119 ASP BB 278 0.0 +279 SQ5n 119 ASP SC1 279 -1.0 +280 SP2 120 VAL BB 280 0.0 +281 SC3 120 VAL SC1 281 0.0 +282 P2 121 GLN BB 282 0.0 +283 P5 121 GLN SC1 283 0.0 +284 SP2 122 ALA BB 284 0.0 +285 TC3 122 ALA SC1 285 0.0 +286 P2 123 TRP BB 286 0.0 +287 TC4 123 TRP SC1 287 0.0 36.0 +288 TN6d 123 TRP SC2 288 0.0 36.0 +289 TC5 123 TRP SC3 289 0.0 0.0 +290 TC5 123 TRP SC4 290 0.0 36.0 +291 TC5 123 TRP SC5 291 0.0 36.0 +292 P2 124 ILE BB 292 0.0 +293 SC2 124 ILE SC1 293 0.0 +294 P2 125 ARG BB 294 0.0 +295 SC3 125 ARG SC1 295 0.0 +296 SQ3p 125 ARG SC2 296 1.0 +297 SP1 126 GLY BB 297 0.0 +298 P2 127 CYS BB 298 0.0 +299 TC6 127 CYS SC1 299 0.0 +300 P2 128 ARG BB 300 0.0 +301 SC3 128 ARG SC1 301 0.0 +302 SQ3p 128 ARG SC2 302 1.0 +303 Q5 129 LEU BB 303 -1 +304 SC2 129 LEU SC1 304 0.0 +305 molecule_0_1 1 LYS CA 305 0 0.0 +306 molecule_0_2 2 VAL CA 306 0 0.0 +307 molecule_0_3 3 PHE CA 307 0 0.0 +308 molecule_0_4 4 GLY CA 308 0 0.0 +309 molecule_0_5 5 ARG CA 309 0 0.0 +310 molecule_0_6 6 CYS CA 310 0 0.0 +311 molecule_0_7 7 GLU CA 311 0 0.0 +312 molecule_0_8 8 LEU CA 312 0 0.0 +313 molecule_0_9 9 ALA CA 313 0 0.0 +314 molecule_0_10 10 ALA CA 314 0 0.0 +315 molecule_0_11 11 ALA CA 315 0 0.0 +316 molecule_0_12 12 MET CA 316 0 0.0 +317 molecule_0_13 13 LYS CA 317 0 0.0 +318 molecule_0_14 14 ARG CA 318 0 0.0 +319 molecule_0_15 15 HIS CA 319 0 0.0 +320 molecule_0_16 16 GLY CA 320 0 0.0 +321 molecule_0_17 17 LEU CA 321 0 0.0 +322 molecule_0_18 18 ASP CA 322 0 0.0 +323 molecule_0_19 19 ASN CA 323 0 0.0 +324 molecule_0_20 20 TYR CA 324 0 0.0 +325 molecule_0_21 21 ARG CA 325 0 0.0 +326 molecule_0_22 22 GLY CA 326 0 0.0 +327 molecule_0_23 23 TYR CA 327 0 0.0 +328 molecule_0_24 24 SER CA 328 0 0.0 +329 molecule_0_25 25 LEU CA 329 0 0.0 +330 molecule_0_26 26 GLY CA 330 0 0.0 +331 molecule_0_27 27 ASN CA 331 0 0.0 +332 molecule_0_28 28 TRP CA 332 0 0.0 +333 molecule_0_29 29 VAL CA 333 0 0.0 +334 molecule_0_30 30 CYS CA 334 0 0.0 +335 molecule_0_31 31 ALA CA 335 0 0.0 +336 molecule_0_32 32 ALA CA 336 0 0.0 +337 molecule_0_33 33 LYS CA 337 0 0.0 +338 molecule_0_34 34 PHE CA 338 0 0.0 +339 molecule_0_35 35 GLU CA 339 0 0.0 +340 molecule_0_36 36 SER CA 340 0 0.0 +341 molecule_0_37 37 ASN CA 341 0 0.0 +342 molecule_0_38 38 PHE CA 342 0 0.0 +343 molecule_0_39 39 ASN CA 343 0 0.0 +344 molecule_0_40 40 THR CA 344 0 0.0 +345 molecule_0_41 41 GLN CA 345 0 0.0 +346 molecule_0_42 42 ALA CA 346 0 0.0 +347 molecule_0_43 43 THR CA 347 0 0.0 +348 molecule_0_44 44 ASN CA 348 0 0.0 +349 molecule_0_45 45 ARG CA 349 0 0.0 +350 molecule_0_46 46 ASN CA 350 0 0.0 +351 molecule_0_47 47 THR CA 351 0 0.0 +352 molecule_0_48 48 ASP CA 352 0 0.0 +353 molecule_0_49 49 GLY CA 353 0 0.0 +354 molecule_0_50 50 SER CA 354 0 0.0 +355 molecule_0_51 51 THR CA 355 0 0.0 +356 molecule_0_52 52 ASP CA 356 0 0.0 +357 molecule_0_53 53 TYR CA 357 0 0.0 +358 molecule_0_54 54 GLY CA 358 0 0.0 +359 molecule_0_55 55 ILE CA 359 0 0.0 +360 molecule_0_56 56 LEU CA 360 0 0.0 +361 molecule_0_57 57 GLN CA 361 0 0.0 +362 molecule_0_58 58 ILE CA 362 0 0.0 +363 molecule_0_59 59 ASN CA 363 0 0.0 +364 molecule_0_60 60 SER CA 364 0 0.0 +365 molecule_0_61 61 ARG CA 365 0 0.0 +366 molecule_0_62 62 TRP CA 366 0 0.0 +367 molecule_0_63 63 TRP CA 367 0 0.0 +368 molecule_0_64 64 CYS CA 368 0 0.0 +369 molecule_0_65 65 ASN CA 369 0 0.0 +370 molecule_0_66 66 ASP CA 370 0 0.0 +371 molecule_0_67 67 GLY CA 371 0 0.0 +372 molecule_0_68 68 ARG CA 372 0 0.0 +373 molecule_0_69 69 THR CA 373 0 0.0 +374 molecule_0_70 70 PRO CA 374 0 0.0 +375 molecule_0_71 71 GLY CA 375 0 0.0 +376 molecule_0_72 72 SER CA 376 0 0.0 +377 molecule_0_73 73 ARG CA 377 0 0.0 +378 molecule_0_74 74 ASN CA 378 0 0.0 +379 molecule_0_75 75 LEU CA 379 0 0.0 +380 molecule_0_76 76 CYS CA 380 0 0.0 +381 molecule_0_77 77 ASN CA 381 0 0.0 +382 molecule_0_78 78 ILE CA 382 0 0.0 +383 molecule_0_79 79 PRO CA 383 0 0.0 +384 molecule_0_80 80 CYS CA 384 0 0.0 +385 molecule_0_81 81 SER CA 385 0 0.0 +386 molecule_0_82 82 ALA CA 386 0 0.0 +387 molecule_0_83 83 LEU CA 387 0 0.0 +388 molecule_0_84 84 LEU CA 388 0 0.0 +389 molecule_0_85 85 SER CA 389 0 0.0 +390 molecule_0_86 86 SER CA 390 0 0.0 +391 molecule_0_87 87 ASP CA 391 0 0.0 +392 molecule_0_88 88 ILE CA 392 0 0.0 +393 molecule_0_89 89 THR CA 393 0 0.0 +394 molecule_0_90 90 ALA CA 394 0 0.0 +395 molecule_0_91 91 SER CA 395 0 0.0 +396 molecule_0_92 92 VAL CA 396 0 0.0 +397 molecule_0_93 93 ASN CA 397 0 0.0 +398 molecule_0_94 94 CYS CA 398 0 0.0 +399 molecule_0_95 95 ALA CA 399 0 0.0 +400 molecule_0_96 96 LYS CA 400 0 0.0 +401 molecule_0_97 97 LYS CA 401 0 0.0 +402 molecule_0_98 98 ILE CA 402 0 0.0 +403 molecule_0_99 99 VAL CA 403 0 0.0 +404 molecule_0_100 100 SER CA 404 0 0.0 +405 molecule_0_101 101 ASP CA 405 0 0.0 +406 molecule_0_102 102 GLY CA 406 0 0.0 +407 molecule_0_103 103 ASN CA 407 0 0.0 +408 molecule_0_104 104 GLY CA 408 0 0.0 +409 molecule_0_105 105 MET CA 409 0 0.0 +410 molecule_0_106 106 ASN CA 410 0 0.0 +411 molecule_0_107 107 ALA CA 411 0 0.0 +412 molecule_0_108 108 TRP CA 412 0 0.0 +413 molecule_0_109 109 VAL CA 413 0 0.0 +414 molecule_0_110 110 ALA CA 414 0 0.0 +415 molecule_0_111 111 TRP CA 415 0 0.0 +416 molecule_0_112 112 ARG CA 416 0 0.0 +417 molecule_0_113 113 ASN CA 417 0 0.0 +418 molecule_0_114 114 ARG CA 418 0 0.0 +419 molecule_0_115 115 CYS CA 419 0 0.0 +420 molecule_0_116 116 LYS CA 420 0 0.0 +421 molecule_0_117 117 GLY CA 421 0 0.0 +422 molecule_0_118 118 THR CA 422 0 0.0 +423 molecule_0_119 119 ASP CA 423 0 0.0 +424 molecule_0_120 120 VAL CA 424 0 0.0 +425 molecule_0_121 121 GLN CA 425 0 0.0 +426 molecule_0_122 122 ALA CA 426 0 0.0 +427 molecule_0_123 123 TRP CA 427 0 0.0 +428 molecule_0_124 124 ILE CA 428 0 0.0 +429 molecule_0_125 125 ARG CA 429 0 0.0 +430 molecule_0_126 126 GLY CA 430 0 0.0 +431 molecule_0_127 127 CYS CA 431 0 0.0 +432 molecule_0_128 128 ARG CA 432 0 0.0 +433 molecule_0_129 129 LEU CA 433 0 0.0 [ bonds ] ; Backbone bonds diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top index b3c77b272..a8528540e 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top @@ -3,10 +3,10 @@ #include "go_atomtypes.itp" #include "go_nbparams.itp" -#include "molecule.itp" +#include "molecule_0.itp" [ system ] Title of the system [ molecules ] -molecule 1 +molecule_0 1 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command index f0de2bf47..5626db7e3 100755 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command @@ -10,3 +10,4 @@ martinize2 -water-bias-eps E:-.5 C:1.0 H:-1.0 -noscfix -cys none +-name molecule_0 \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp index 3b028c477..bcbcf6145 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp @@ -1,130 +1,130 @@ [ atomtypes ] -molecule_1 0.0 0 A 0.00000000 0.00000000 -molecule_2 0.0 0 A 0.00000000 0.00000000 -molecule_3 0.0 0 A 0.00000000 0.00000000 -molecule_4 0.0 0 A 0.00000000 0.00000000 -molecule_5 0.0 0 A 0.00000000 0.00000000 -molecule_6 0.0 0 A 0.00000000 0.00000000 -molecule_7 0.0 0 A 0.00000000 0.00000000 -molecule_8 0.0 0 A 0.00000000 0.00000000 -molecule_9 0.0 0 A 0.00000000 0.00000000 -molecule_10 0.0 0 A 0.00000000 0.00000000 -molecule_11 0.0 0 A 0.00000000 0.00000000 -molecule_12 0.0 0 A 0.00000000 0.00000000 -molecule_13 0.0 0 A 0.00000000 0.00000000 -molecule_14 0.0 0 A 0.00000000 0.00000000 -molecule_15 0.0 0 A 0.00000000 0.00000000 -molecule_16 0.0 0 A 0.00000000 0.00000000 -molecule_17 0.0 0 A 0.00000000 0.00000000 -molecule_18 0.0 0 A 0.00000000 0.00000000 -molecule_19 0.0 0 A 0.00000000 0.00000000 -molecule_20 0.0 0 A 0.00000000 0.00000000 -molecule_21 0.0 0 A 0.00000000 0.00000000 -molecule_22 0.0 0 A 0.00000000 0.00000000 -molecule_23 0.0 0 A 0.00000000 0.00000000 -molecule_24 0.0 0 A 0.00000000 0.00000000 -molecule_25 0.0 0 A 0.00000000 0.00000000 -molecule_26 0.0 0 A 0.00000000 0.00000000 -molecule_27 0.0 0 A 0.00000000 0.00000000 -molecule_28 0.0 0 A 0.00000000 0.00000000 -molecule_29 0.0 0 A 0.00000000 0.00000000 -molecule_30 0.0 0 A 0.00000000 0.00000000 -molecule_31 0.0 0 A 0.00000000 0.00000000 -molecule_32 0.0 0 A 0.00000000 0.00000000 -molecule_33 0.0 0 A 0.00000000 0.00000000 -molecule_34 0.0 0 A 0.00000000 0.00000000 -molecule_35 0.0 0 A 0.00000000 0.00000000 -molecule_36 0.0 0 A 0.00000000 0.00000000 -molecule_37 0.0 0 A 0.00000000 0.00000000 -molecule_38 0.0 0 A 0.00000000 0.00000000 -molecule_39 0.0 0 A 0.00000000 0.00000000 -molecule_40 0.0 0 A 0.00000000 0.00000000 -molecule_41 0.0 0 A 0.00000000 0.00000000 -molecule_42 0.0 0 A 0.00000000 0.00000000 -molecule_43 0.0 0 A 0.00000000 0.00000000 -molecule_44 0.0 0 A 0.00000000 0.00000000 -molecule_45 0.0 0 A 0.00000000 0.00000000 -molecule_46 0.0 0 A 0.00000000 0.00000000 -molecule_47 0.0 0 A 0.00000000 0.00000000 -molecule_48 0.0 0 A 0.00000000 0.00000000 -molecule_49 0.0 0 A 0.00000000 0.00000000 -molecule_50 0.0 0 A 0.00000000 0.00000000 -molecule_51 0.0 0 A 0.00000000 0.00000000 -molecule_52 0.0 0 A 0.00000000 0.00000000 -molecule_53 0.0 0 A 0.00000000 0.00000000 -molecule_54 0.0 0 A 0.00000000 0.00000000 -molecule_55 0.0 0 A 0.00000000 0.00000000 -molecule_56 0.0 0 A 0.00000000 0.00000000 -molecule_57 0.0 0 A 0.00000000 0.00000000 -molecule_58 0.0 0 A 0.00000000 0.00000000 -molecule_59 0.0 0 A 0.00000000 0.00000000 -molecule_60 0.0 0 A 0.00000000 0.00000000 -molecule_61 0.0 0 A 0.00000000 0.00000000 -molecule_62 0.0 0 A 0.00000000 0.00000000 -molecule_63 0.0 0 A 0.00000000 0.00000000 -molecule_64 0.0 0 A 0.00000000 0.00000000 -molecule_65 0.0 0 A 0.00000000 0.00000000 -molecule_66 0.0 0 A 0.00000000 0.00000000 -molecule_67 0.0 0 A 0.00000000 0.00000000 -molecule_68 0.0 0 A 0.00000000 0.00000000 -molecule_69 0.0 0 A 0.00000000 0.00000000 -molecule_70 0.0 0 A 0.00000000 0.00000000 -molecule_71 0.0 0 A 0.00000000 0.00000000 -molecule_72 0.0 0 A 0.00000000 0.00000000 -molecule_73 0.0 0 A 0.00000000 0.00000000 -molecule_74 0.0 0 A 0.00000000 0.00000000 -molecule_75 0.0 0 A 0.00000000 0.00000000 -molecule_76 0.0 0 A 0.00000000 0.00000000 -molecule_77 0.0 0 A 0.00000000 0.00000000 -molecule_78 0.0 0 A 0.00000000 0.00000000 -molecule_79 0.0 0 A 0.00000000 0.00000000 -molecule_80 0.0 0 A 0.00000000 0.00000000 -molecule_81 0.0 0 A 0.00000000 0.00000000 -molecule_82 0.0 0 A 0.00000000 0.00000000 -molecule_83 0.0 0 A 0.00000000 0.00000000 -molecule_84 0.0 0 A 0.00000000 0.00000000 -molecule_85 0.0 0 A 0.00000000 0.00000000 -molecule_86 0.0 0 A 0.00000000 0.00000000 -molecule_87 0.0 0 A 0.00000000 0.00000000 -molecule_88 0.0 0 A 0.00000000 0.00000000 -molecule_89 0.0 0 A 0.00000000 0.00000000 -molecule_90 0.0 0 A 0.00000000 0.00000000 -molecule_91 0.0 0 A 0.00000000 0.00000000 -molecule_92 0.0 0 A 0.00000000 0.00000000 -molecule_93 0.0 0 A 0.00000000 0.00000000 -molecule_94 0.0 0 A 0.00000000 0.00000000 -molecule_95 0.0 0 A 0.00000000 0.00000000 -molecule_96 0.0 0 A 0.00000000 0.00000000 -molecule_97 0.0 0 A 0.00000000 0.00000000 -molecule_98 0.0 0 A 0.00000000 0.00000000 -molecule_99 0.0 0 A 0.00000000 0.00000000 -molecule_100 0.0 0 A 0.00000000 0.00000000 -molecule_101 0.0 0 A 0.00000000 0.00000000 -molecule_102 0.0 0 A 0.00000000 0.00000000 -molecule_103 0.0 0 A 0.00000000 0.00000000 -molecule_104 0.0 0 A 0.00000000 0.00000000 -molecule_105 0.0 0 A 0.00000000 0.00000000 -molecule_106 0.0 0 A 0.00000000 0.00000000 -molecule_107 0.0 0 A 0.00000000 0.00000000 -molecule_108 0.0 0 A 0.00000000 0.00000000 -molecule_109 0.0 0 A 0.00000000 0.00000000 -molecule_110 0.0 0 A 0.00000000 0.00000000 -molecule_111 0.0 0 A 0.00000000 0.00000000 -molecule_112 0.0 0 A 0.00000000 0.00000000 -molecule_113 0.0 0 A 0.00000000 0.00000000 -molecule_114 0.0 0 A 0.00000000 0.00000000 -molecule_115 0.0 0 A 0.00000000 0.00000000 -molecule_116 0.0 0 A 0.00000000 0.00000000 -molecule_117 0.0 0 A 0.00000000 0.00000000 -molecule_118 0.0 0 A 0.00000000 0.00000000 -molecule_119 0.0 0 A 0.00000000 0.00000000 -molecule_120 0.0 0 A 0.00000000 0.00000000 -molecule_121 0.0 0 A 0.00000000 0.00000000 -molecule_122 0.0 0 A 0.00000000 0.00000000 -molecule_123 0.0 0 A 0.00000000 0.00000000 -molecule_124 0.0 0 A 0.00000000 0.00000000 -molecule_125 0.0 0 A 0.00000000 0.00000000 -molecule_126 0.0 0 A 0.00000000 0.00000000 -molecule_127 0.0 0 A 0.00000000 0.00000000 -molecule_128 0.0 0 A 0.00000000 0.00000000 -molecule_129 0.0 0 A 0.00000000 0.00000000 +molecule_0_1 0.0 0 A 0.00000000 0.00000000 +molecule_0_2 0.0 0 A 0.00000000 0.00000000 +molecule_0_3 0.0 0 A 0.00000000 0.00000000 +molecule_0_4 0.0 0 A 0.00000000 0.00000000 +molecule_0_5 0.0 0 A 0.00000000 0.00000000 +molecule_0_6 0.0 0 A 0.00000000 0.00000000 +molecule_0_7 0.0 0 A 0.00000000 0.00000000 +molecule_0_8 0.0 0 A 0.00000000 0.00000000 +molecule_0_9 0.0 0 A 0.00000000 0.00000000 +molecule_0_10 0.0 0 A 0.00000000 0.00000000 +molecule_0_11 0.0 0 A 0.00000000 0.00000000 +molecule_0_12 0.0 0 A 0.00000000 0.00000000 +molecule_0_13 0.0 0 A 0.00000000 0.00000000 +molecule_0_14 0.0 0 A 0.00000000 0.00000000 +molecule_0_15 0.0 0 A 0.00000000 0.00000000 +molecule_0_16 0.0 0 A 0.00000000 0.00000000 +molecule_0_17 0.0 0 A 0.00000000 0.00000000 +molecule_0_18 0.0 0 A 0.00000000 0.00000000 +molecule_0_19 0.0 0 A 0.00000000 0.00000000 +molecule_0_20 0.0 0 A 0.00000000 0.00000000 +molecule_0_21 0.0 0 A 0.00000000 0.00000000 +molecule_0_22 0.0 0 A 0.00000000 0.00000000 +molecule_0_23 0.0 0 A 0.00000000 0.00000000 +molecule_0_24 0.0 0 A 0.00000000 0.00000000 +molecule_0_25 0.0 0 A 0.00000000 0.00000000 +molecule_0_26 0.0 0 A 0.00000000 0.00000000 +molecule_0_27 0.0 0 A 0.00000000 0.00000000 +molecule_0_28 0.0 0 A 0.00000000 0.00000000 +molecule_0_29 0.0 0 A 0.00000000 0.00000000 +molecule_0_30 0.0 0 A 0.00000000 0.00000000 +molecule_0_31 0.0 0 A 0.00000000 0.00000000 +molecule_0_32 0.0 0 A 0.00000000 0.00000000 +molecule_0_33 0.0 0 A 0.00000000 0.00000000 +molecule_0_34 0.0 0 A 0.00000000 0.00000000 +molecule_0_35 0.0 0 A 0.00000000 0.00000000 +molecule_0_36 0.0 0 A 0.00000000 0.00000000 +molecule_0_37 0.0 0 A 0.00000000 0.00000000 +molecule_0_38 0.0 0 A 0.00000000 0.00000000 +molecule_0_39 0.0 0 A 0.00000000 0.00000000 +molecule_0_40 0.0 0 A 0.00000000 0.00000000 +molecule_0_41 0.0 0 A 0.00000000 0.00000000 +molecule_0_42 0.0 0 A 0.00000000 0.00000000 +molecule_0_43 0.0 0 A 0.00000000 0.00000000 +molecule_0_44 0.0 0 A 0.00000000 0.00000000 +molecule_0_45 0.0 0 A 0.00000000 0.00000000 +molecule_0_46 0.0 0 A 0.00000000 0.00000000 +molecule_0_47 0.0 0 A 0.00000000 0.00000000 +molecule_0_48 0.0 0 A 0.00000000 0.00000000 +molecule_0_49 0.0 0 A 0.00000000 0.00000000 +molecule_0_50 0.0 0 A 0.00000000 0.00000000 +molecule_0_51 0.0 0 A 0.00000000 0.00000000 +molecule_0_52 0.0 0 A 0.00000000 0.00000000 +molecule_0_53 0.0 0 A 0.00000000 0.00000000 +molecule_0_54 0.0 0 A 0.00000000 0.00000000 +molecule_0_55 0.0 0 A 0.00000000 0.00000000 +molecule_0_56 0.0 0 A 0.00000000 0.00000000 +molecule_0_57 0.0 0 A 0.00000000 0.00000000 +molecule_0_58 0.0 0 A 0.00000000 0.00000000 +molecule_0_59 0.0 0 A 0.00000000 0.00000000 +molecule_0_60 0.0 0 A 0.00000000 0.00000000 +molecule_0_61 0.0 0 A 0.00000000 0.00000000 +molecule_0_62 0.0 0 A 0.00000000 0.00000000 +molecule_0_63 0.0 0 A 0.00000000 0.00000000 +molecule_0_64 0.0 0 A 0.00000000 0.00000000 +molecule_0_65 0.0 0 A 0.00000000 0.00000000 +molecule_0_66 0.0 0 A 0.00000000 0.00000000 +molecule_0_67 0.0 0 A 0.00000000 0.00000000 +molecule_0_68 0.0 0 A 0.00000000 0.00000000 +molecule_0_69 0.0 0 A 0.00000000 0.00000000 +molecule_0_70 0.0 0 A 0.00000000 0.00000000 +molecule_0_71 0.0 0 A 0.00000000 0.00000000 +molecule_0_72 0.0 0 A 0.00000000 0.00000000 +molecule_0_73 0.0 0 A 0.00000000 0.00000000 +molecule_0_74 0.0 0 A 0.00000000 0.00000000 +molecule_0_75 0.0 0 A 0.00000000 0.00000000 +molecule_0_76 0.0 0 A 0.00000000 0.00000000 +molecule_0_77 0.0 0 A 0.00000000 0.00000000 +molecule_0_78 0.0 0 A 0.00000000 0.00000000 +molecule_0_79 0.0 0 A 0.00000000 0.00000000 +molecule_0_80 0.0 0 A 0.00000000 0.00000000 +molecule_0_81 0.0 0 A 0.00000000 0.00000000 +molecule_0_82 0.0 0 A 0.00000000 0.00000000 +molecule_0_83 0.0 0 A 0.00000000 0.00000000 +molecule_0_84 0.0 0 A 0.00000000 0.00000000 +molecule_0_85 0.0 0 A 0.00000000 0.00000000 +molecule_0_86 0.0 0 A 0.00000000 0.00000000 +molecule_0_87 0.0 0 A 0.00000000 0.00000000 +molecule_0_88 0.0 0 A 0.00000000 0.00000000 +molecule_0_89 0.0 0 A 0.00000000 0.00000000 +molecule_0_90 0.0 0 A 0.00000000 0.00000000 +molecule_0_91 0.0 0 A 0.00000000 0.00000000 +molecule_0_92 0.0 0 A 0.00000000 0.00000000 +molecule_0_93 0.0 0 A 0.00000000 0.00000000 +molecule_0_94 0.0 0 A 0.00000000 0.00000000 +molecule_0_95 0.0 0 A 0.00000000 0.00000000 +molecule_0_96 0.0 0 A 0.00000000 0.00000000 +molecule_0_97 0.0 0 A 0.00000000 0.00000000 +molecule_0_98 0.0 0 A 0.00000000 0.00000000 +molecule_0_99 0.0 0 A 0.00000000 0.00000000 +molecule_0_100 0.0 0 A 0.00000000 0.00000000 +molecule_0_101 0.0 0 A 0.00000000 0.00000000 +molecule_0_102 0.0 0 A 0.00000000 0.00000000 +molecule_0_103 0.0 0 A 0.00000000 0.00000000 +molecule_0_104 0.0 0 A 0.00000000 0.00000000 +molecule_0_105 0.0 0 A 0.00000000 0.00000000 +molecule_0_106 0.0 0 A 0.00000000 0.00000000 +molecule_0_107 0.0 0 A 0.00000000 0.00000000 +molecule_0_108 0.0 0 A 0.00000000 0.00000000 +molecule_0_109 0.0 0 A 0.00000000 0.00000000 +molecule_0_110 0.0 0 A 0.00000000 0.00000000 +molecule_0_111 0.0 0 A 0.00000000 0.00000000 +molecule_0_112 0.0 0 A 0.00000000 0.00000000 +molecule_0_113 0.0 0 A 0.00000000 0.00000000 +molecule_0_114 0.0 0 A 0.00000000 0.00000000 +molecule_0_115 0.0 0 A 0.00000000 0.00000000 +molecule_0_116 0.0 0 A 0.00000000 0.00000000 +molecule_0_117 0.0 0 A 0.00000000 0.00000000 +molecule_0_118 0.0 0 A 0.00000000 0.00000000 +molecule_0_119 0.0 0 A 0.00000000 0.00000000 +molecule_0_120 0.0 0 A 0.00000000 0.00000000 +molecule_0_121 0.0 0 A 0.00000000 0.00000000 +molecule_0_122 0.0 0 A 0.00000000 0.00000000 +molecule_0_123 0.0 0 A 0.00000000 0.00000000 +molecule_0_124 0.0 0 A 0.00000000 0.00000000 +molecule_0_125 0.0 0 A 0.00000000 0.00000000 +molecule_0_126 0.0 0 A 0.00000000 0.00000000 +molecule_0_127 0.0 0 A 0.00000000 0.00000000 +molecule_0_128 0.0 0 A 0.00000000 0.00000000 +molecule_0_129 0.0 0 A 0.00000000 0.00000000 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp index 1fb4a6712..1d80a41dd 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp @@ -1,293 +1,305 @@ [ nonbond_params ] -molecule_7 molecule_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 -molecule_8 molecule_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 -molecule_8 molecule_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 -molecule_9 molecule_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 -molecule_10 molecule_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 -molecule_11 molecule_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 -molecule_12 molecule_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 -molecule_13 molecule_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 -molecule_14 molecule_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 -molecule_15 molecule_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 -molecule_16 molecule_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 -molecule_17 molecule_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 -molecule_18 molecule_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 -molecule_20 molecule_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 -molecule_23 molecule_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 -molecule_24 molecule_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 -molecule_24 molecule_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 -molecule_25 molecule_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 -molecule_25 molecule_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 -molecule_25 molecule_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 -molecule_25 molecule_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 -molecule_27 molecule_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 -molecule_27 molecule_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 -molecule_28 molecule_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 -molecule_28 molecule_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 -molecule_28 molecule_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 -molecule_28 molecule_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 -molecule_29 molecule_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 -molecule_29 molecule_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 -molecule_29 molecule_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 -molecule_29 molecule_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 -molecule_30 molecule_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 -molecule_31 molecule_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 -molecule_32 molecule_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 -molecule_32 molecule_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 -molecule_33 molecule_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 -molecule_34 molecule_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 -molecule_35 molecule_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 -molecule_36 molecule_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 -molecule_37 molecule_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 -molecule_37 molecule_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 -molecule_38 molecule_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 -molecule_38 molecule_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 -molecule_38 molecule_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 -molecule_38 molecule_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 -molecule_38 molecule_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 -molecule_38 molecule_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 -molecule_38 molecule_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 -molecule_38 molecule_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 -molecule_39 molecule_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 -molecule_39 molecule_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 -molecule_40 molecule_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 -molecule_40 molecule_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 -molecule_41 molecule_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 -molecule_42 molecule_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 -molecule_44 molecule_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 -molecule_49 molecule_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 -molecule_50 molecule_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 -molecule_50 molecule_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 -molecule_51 molecule_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 -molecule_51 molecule_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 -molecule_51 molecule_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 -molecule_51 molecule_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 -molecule_52 molecule_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 -molecule_52 molecule_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 -molecule_52 molecule_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 -molecule_53 molecule_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 -molecule_53 molecule_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 -molecule_54 molecule_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 -molecule_54 molecule_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 -molecule_54 molecule_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 -molecule_55 molecule_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 -molecule_55 molecule_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 -molecule_55 molecule_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 -molecule_55 molecule_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 -molecule_55 molecule_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 -molecule_55 molecule_38 1 0.53863592 9.41400000 ;go bond 0.6045983765957093 -molecule_55 molecule_39 1 0.46884965 9.41400000 ;go bond 0.5262659343028784 -molecule_55 molecule_40 1 0.49397051 9.41400000 ;go bond 0.5544631488965023 -molecule_56 molecule_31 1 0.63305577 9.41400000 ;go bond 0.7105810801311345 -molecule_56 molecule_32 1 0.57070473 9.41400000 ;go bond 0.6405943964432239 -molecule_56 molecule_35 1 0.54499611 9.41400000 ;go bond 0.6117374504966917 -molecule_57 molecule_35 1 0.59142457 9.41400000 ;go bond 0.6638516326030536 -molecule_57 molecule_36 1 0.73443635 9.41400000 ;go bond 0.8243769340599911 -molecule_57 molecule_42 1 0.68123116 9.41400000 ;go bond 0.7646561231921536 -molecule_57 molecule_43 1 0.72932038 9.41400000 ;go bond 0.8186344517277264 -molecule_57 molecule_44 1 0.71017360 9.41400000 ;go bond 0.7971429108051539 -molecule_57 molecule_52 1 0.45255106 9.41400000 ;go bond 0.5079713907835711 -molecule_57 molecule_53 1 0.35572883 9.41400000 ;go bond 0.3992921109620664 -molecule_58 molecule_52 1 0.41486867 9.41400000 ;go bond 0.4656743363160884 -molecule_58 molecule_53 1 0.33528745 9.41400000 ;go bond 0.37634743770658646 -molecule_59 molecule_46 1 0.92985190 9.41400000 ;go bond 1.0437234628284975 -molecule_59 molecule_50 1 0.67865311 9.41400000 ;go bond 0.7617623567683692 -molecule_59 molecule_51 1 0.46599015 9.41400000 ;go bond 0.5230562584392384 -molecule_59 molecule_52 1 0.52411606 9.41400000 ;go bond 0.5883003833904864 -molecule_60 molecule_50 1 0.55757626 9.41400000 ;go bond 0.6258581889054639 -molecule_60 molecule_51 1 0.45353930 9.41400000 ;go bond 0.5090806492037284 -molecule_60 molecule_53 1 0.78554721 9.41400000 ;go bond 0.8817469319963909 -molecule_61 molecule_48 1 0.83253174 9.41400000 ;go bond 0.9344852838875899 -molecule_61 molecule_50 1 0.65515556 9.41400000 ;go bond 0.7353872567523113 -molecule_63 molecule_58 1 0.62967119 9.41400000 ;go bond 0.7067820082223201 -molecule_63 molecule_59 1 0.46427561 9.41400000 ;go bond 0.521131754230626 -molecule_64 molecule_53 1 0.82959737 9.41400000 ;go bond 0.9311915604701376 -molecule_64 molecule_60 1 0.38156281 9.41400000 ;go bond 0.4282897748904594 -molecule_66 molecule_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 -molecule_66 molecule_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 -molecule_68 molecule_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 -molecule_69 molecule_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 -molecule_69 molecule_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 -molecule_69 molecule_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 -molecule_69 molecule_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 -molecule_70 molecule_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 -molecule_72 molecule_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 -molecule_72 molecule_61 1 0.44682674 9.41400000 ;go bond 0.5015460538054222 -molecule_72 molecule_64 1 0.62949829 9.41400000 ;go bond 0.7065879353028186 -molecule_73 molecule_61 1 0.53130673 9.41400000 ;go bond 0.5963716385459682 -molecule_73 molecule_62 1 0.40729971 9.41400000 ;go bond 0.4571784705977002 -molecule_74 molecule_62 1 0.44897571 9.41400000 ;go bond 0.5039581950921611 -molecule_74 molecule_63 1 0.38506256 9.41400000 ;go bond 0.43221810950469636 -molecule_74 molecule_64 1 0.43052761 9.41400000 ;go bond 0.4832509069633833 -molecule_74 molecule_65 1 0.61184241 9.41400000 ;go bond 0.6867698876930867 -molecule_75 molecule_62 1 0.52199782 9.41400000 ;go bond 0.5859227452973559 -molecule_75 molecule_63 1 0.40610455 9.41400000 ;go bond 0.45583694740556885 -molecule_76 molecule_63 1 0.46409225 9.41400000 ;go bond 0.5209259369461889 -molecule_78 molecule_63 1 0.57576077 9.41400000 ;go bond 0.6462696105707938 -molecule_78 molecule_65 1 0.43974215 9.41400000 ;go bond 0.4935938729629976 -molecule_78 molecule_74 1 0.56052614 9.41400000 ;go bond 0.6291693208239874 -molecule_80 molecule_53 1 0.60673469 9.41400000 ;go bond 0.6810366626079589 -molecule_80 molecule_60 1 0.73868742 9.41400000 ;go bond 0.8291485950674535 -molecule_82 molecule_78 1 0.66632073 9.41400000 ;go bond 0.7479197331826131 -molecule_83 molecule_53 1 0.51788905 9.41400000 ;go bond 0.581310806103053 -molecule_83 molecule_54 1 0.51088855 9.41400000 ;go bond 0.5734530137551908 -molecule_83 molecule_58 1 0.70980394 9.41400000 ;go bond 0.7967279839859979 -molecule_83 molecule_64 1 0.89499397 9.41400000 ;go bond 1.0045967605887745 -molecule_83 molecule_78 1 0.81556181 9.41400000 ;go bond 0.9154371804917103 -molecule_84 molecule_40 1 0.40226578 9.41400000 ;go bond 0.45152806893595954 -molecule_84 molecule_41 1 0.48796771 9.41400000 ;go bond 0.5477252325235119 -molecule_84 molecule_42 1 0.63252675 9.41400000 ;go bond 0.7099872721863867 -molecule_84 molecule_43 1 0.89270990 9.41400000 ;go bond 1.0020329775751635 -molecule_84 molecule_53 1 0.66502200 9.41400000 ;go bond 0.7464619538686407 -molecule_84 molecule_54 1 0.56665258 9.41400000 ;go bond 0.6360460147186728 -molecule_85 molecule_40 1 0.48170210 9.41400000 ;go bond 0.5406923273735796 -molecule_85 molecule_81 1 0.64785523 9.41400000 ;go bond 0.7271929039256984 -molecule_86 molecule_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 -molecule_86 molecule_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 -molecule_86 molecule_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 -molecule_88 molecule_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 -molecule_88 molecule_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 -molecule_88 molecule_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 -molecule_88 molecule_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 -molecule_88 molecule_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 -molecule_88 molecule_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 -molecule_89 molecule_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 -molecule_89 molecule_15 1 0.69215886 9.41400000 ;go bond 0.7769220558398894 -molecule_90 molecule_78 1 0.80563795 9.41400000 ;go bond 0.9042980239792853 -molecule_90 molecule_82 1 0.59740893 9.41400000 ;go bond 0.6705688513824994 -molecule_90 molecule_83 1 0.57714934 9.41400000 ;go bond 0.6478282257424317 -molecule_91 molecule_55 1 0.70847337 9.41400000 ;go bond 0.7952344695348353 -molecule_91 molecule_58 1 0.76773720 9.41400000 ;go bond 0.8617558647944001 -molecule_91 molecule_83 1 0.57795007 9.41400000 ;go bond 0.6487270215620753 -molecule_92 molecule_15 1 0.66057405 9.41400000 ;go bond 0.741469302181026 -molecule_92 molecule_17 1 0.76276340 9.41400000 ;go bond 0.8561729710147924 -molecule_92 molecule_88 1 0.55891711 9.41400000 ;go bond 0.6273632448163519 -molecule_93 molecule_89 1 0.55091233 9.41400000 ;go bond 0.6183781864423775 -molecule_94 molecule_58 1 0.80192436 9.41400000 ;go bond 0.9001296640477775 -molecule_94 molecule_63 1 0.69400655 9.41400000 ;go bond 0.7789960144450432 -molecule_94 molecule_83 1 0.89829847 9.41400000 ;go bond 1.0083059444227724 -molecule_94 molecule_90 1 0.53696870 9.41400000 ;go bond 0.6027269866522963 -molecule_95 molecule_28 1 0.94028879 9.41400000 ;go bond 1.0554384813372668 -molecule_95 molecule_56 1 0.76727508 9.41400000 ;go bond 0.8612371596953154 -molecule_95 molecule_58 1 0.83998475 9.41400000 ;go bond 0.9428510053550558 -molecule_95 molecule_91 1 0.53148309 9.41400000 ;go bond 0.5965695928114466 -molecule_96 molecule_15 1 0.94537258 9.41400000 ;go bond 1.0611448446580265 -molecule_96 molecule_16 1 0.84805127 9.41400000 ;go bond 0.9519053644995195 -molecule_96 molecule_17 1 0.81454872 9.41400000 ;go bond 0.9143000281459933 -molecule_96 molecule_20 1 0.73587759 9.41400000 ;go bond 0.8259946673768416 -molecule_96 molecule_92 1 0.54860993 9.41400000 ;go bond 0.6157938252917854 -molecule_97 molecule_63 1 0.84557275 9.41400000 ;go bond 0.9491233248865086 -molecule_97 molecule_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 -molecule_97 molecule_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 -molecule_98 molecule_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 -molecule_98 molecule_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 -molecule_98 molecule_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 -molecule_99 molecule_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 -molecule_99 molecule_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 -molecule_99 molecule_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 -molecule_99 molecule_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 -molecule_100 molecule_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 -molecule_100 molecule_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 -molecule_100 molecule_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 -molecule_101 molecule_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 -molecule_104 molecule_23 1 0.90496194 9.41400000 ;go bond 1.0157854279713863 -molecule_104 molecule_99 1 0.37779975 9.41400000 ;go bond 0.42406587714866395 -molecule_105 molecule_23 1 0.85792539 9.41400000 ;go bond 0.9629886926477136 -molecule_105 molecule_27 1 0.80028132 9.41400000 ;go bond 0.8982854095190085 -molecule_105 molecule_28 1 0.85914649 9.41400000 ;go bond 0.9643593287596212 -molecule_105 molecule_31 1 0.84674626 9.41400000 ;go bond 0.950440544780807 -molecule_105 molecule_99 1 0.58741430 9.41400000 ;go bond 0.6593502594081683 -molecule_107 molecule_98 1 0.70183885 9.41400000 ;go bond 0.7877874714268905 -molecule_108 molecule_28 1 0.92956079 9.41400000 ;go bond 1.0433967044744268 -molecule_108 molecule_35 1 0.82960839 9.41400000 ;go bond 0.9312039368635526 -molecule_108 molecule_56 1 0.78133210 9.41400000 ;go bond 0.8770156294387439 -molecule_108 molecule_57 1 0.77168204 9.41400000 ;go bond 0.8661838041857776 -molecule_108 molecule_98 1 0.90403083 9.41400000 ;go bond 1.014740292066367 -molecule_108 molecule_99 1 0.90315750 9.41400000 ;go bond 1.0137600206889819 -molecule_110 molecule_34 1 0.54869664 9.41400000 ;go bond 0.6158911542488904 -molecule_110 molecule_35 1 0.64980269 9.41400000 ;go bond 0.7293788607697123 -molecule_111 molecule_27 1 0.70311941 9.41400000 ;go bond 0.7892248529963473 -molecule_111 molecule_31 1 0.56259884 9.41400000 ;go bond 0.6314958500157425 -molecule_111 molecule_105 1 0.59346888 9.41400000 ;go bond 0.6661462995266982 -molecule_111 molecule_106 1 0.59882239 9.41400000 ;go bond 0.6721554100763635 -molecule_112 molecule_106 1 0.57753815 9.41400000 ;go bond 0.6482646568405853 -molecule_112 molecule_107 1 0.74260248 9.41400000 ;go bond 0.833543103918769 -molecule_112 molecule_108 1 0.53753958 9.41400000 ;go bond 0.603367775987529 -molecule_113 molecule_109 1 0.53306219 9.41400000 ;go bond 0.5983420831461288 -molecule_114 molecule_34 1 0.72771145 9.41400000 ;go bond 0.8168284821715603 -molecule_114 molecule_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 -molecule_115 molecule_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 -molecule_115 molecule_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 -molecule_115 molecule_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 -molecule_116 molecule_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 -molecule_116 molecule_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 -molecule_116 molecule_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 -molecule_118 molecule_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 -molecule_120 molecule_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 -molecule_120 molecule_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 -molecule_120 molecule_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 -molecule_120 molecule_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 -molecule_120 molecule_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 -molecule_122 molecule_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 -molecule_123 molecule_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 -molecule_123 molecule_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 -molecule_123 molecule_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 -molecule_123 molecule_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 -molecule_123 molecule_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 -molecule_123 molecule_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 -molecule_124 molecule_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 -molecule_124 molecule_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 -molecule_124 molecule_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 -molecule_124 molecule_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 -molecule_124 molecule_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 -molecule_125 molecule_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 -molecule_125 molecule_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 -molecule_129 molecule_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 -molecule_129 molecule_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 -molecule_129 molecule_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 -molecule_129 molecule_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 -W molecule_1 1 0.47000000 1.00000000 ;water bias C -W molecule_2 1 0.41000000 -0.50000000 ;water bias E -W molecule_3 1 0.47000000 1.00000000 ;water bias C -W molecule_4 1 0.41000000 1.00000000 ;water bias C -W molecule_9 1 0.41000000 -1.00000000 ;water bias H -W molecule_10 1 0.41000000 -1.00000000 ;water bias H -W molecule_17 1 0.47000000 1.00000000 ;water bias C -W molecule_20 1 0.47000000 -0.50000000 ;water bias E -W molecule_23 1 0.47000000 -0.50000000 ;water bias E -W molecule_24 1 0.47000000 1.00000000 ;water bias C -W molecule_29 1 0.41000000 -1.00000000 ;water bias H -W molecule_30 1 0.47000000 -1.00000000 ;water bias H -W molecule_31 1 0.41000000 -1.00000000 ;water bias H -W molecule_32 1 0.41000000 -1.00000000 ;water bias H -W molecule_39 1 0.47000000 -0.50000000 ;water bias E -W molecule_42 1 0.41000000 1.00000000 ;water bias C -W molecule_43 1 0.47000000 -0.50000000 ;water bias E -W molecule_44 1 0.47000000 -0.50000000 ;water bias E -W molecule_45 1 0.47000000 -0.50000000 ;water bias E -W molecule_46 1 0.47000000 1.00000000 ;water bias C -W molecule_50 1 0.47000000 1.00000000 ;water bias C -W molecule_51 1 0.47000000 -0.50000000 ;water bias E -W molecule_52 1 0.47000000 -0.50000000 ;water bias E -W molecule_53 1 0.47000000 -0.50000000 ;water bias E -W molecule_58 1 0.47000000 -0.50000000 ;water bias E -W molecule_59 1 0.47000000 -0.50000000 ;water bias E -W molecule_64 1 0.47000000 1.00000000 ;water bias C -W molecule_65 1 0.47000000 -0.50000000 ;water bias E -W molecule_66 1 0.47000000 1.00000000 ;water bias C -W molecule_68 1 0.47000000 1.00000000 ;water bias C -W molecule_69 1 0.47000000 1.00000000 ;water bias C -W molecule_72 1 0.47000000 1.00000000 ;water bias C -W molecule_73 1 0.47000000 1.00000000 ;water bias C -W molecule_74 1 0.47000000 1.00000000 ;water bias C -W molecule_77 1 0.47000000 1.00000000 ;water bias C -W molecule_79 1 0.41000000 -0.50000000 ;water bias E -W molecule_88 1 0.47000000 1.00000000 ;water bias C -W molecule_93 1 0.47000000 -1.00000000 ;water bias H -W molecule_94 1 0.47000000 -1.00000000 ;water bias H -W molecule_95 1 0.41000000 -1.00000000 ;water bias H -W molecule_96 1 0.47000000 -1.00000000 ;water bias H -W molecule_119 1 0.47000000 1.00000000 ;water bias C -W molecule_127 1 0.47000000 1.00000000 ;water bias C -W molecule_128 1 0.47000000 1.00000000 ;water bias C -W molecule_129 1 0.47000000 1.00000000 ;water bias C +molecule_0_7 molecule_0_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 +molecule_0_8 molecule_0_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 +molecule_0_8 molecule_0_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 +molecule_0_9 molecule_0_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 +molecule_0_10 molecule_0_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 +molecule_0_11 molecule_0_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 +molecule_0_12 molecule_0_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 +molecule_0_13 molecule_0_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 +molecule_0_14 molecule_0_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 +molecule_0_15 molecule_0_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 +molecule_0_16 molecule_0_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 +molecule_0_17 molecule_0_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 +molecule_0_18 molecule_0_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 +molecule_0_20 molecule_0_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 +molecule_0_23 molecule_0_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 +molecule_0_24 molecule_0_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 +molecule_0_24 molecule_0_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 +molecule_0_25 molecule_0_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 +molecule_0_25 molecule_0_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 +molecule_0_25 molecule_0_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 +molecule_0_25 molecule_0_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 +molecule_0_27 molecule_0_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 +molecule_0_27 molecule_0_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 +molecule_0_28 molecule_0_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 +molecule_0_28 molecule_0_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 +molecule_0_28 molecule_0_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 +molecule_0_28 molecule_0_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 +molecule_0_29 molecule_0_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 +molecule_0_29 molecule_0_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 +molecule_0_29 molecule_0_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 +molecule_0_29 molecule_0_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 +molecule_0_30 molecule_0_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 +molecule_0_31 molecule_0_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 +molecule_0_32 molecule_0_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 +molecule_0_32 molecule_0_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 +molecule_0_33 molecule_0_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 +molecule_0_34 molecule_0_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 +molecule_0_35 molecule_0_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 +molecule_0_36 molecule_0_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 +molecule_0_37 molecule_0_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 +molecule_0_37 molecule_0_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 +molecule_0_38 molecule_0_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 +molecule_0_38 molecule_0_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 +molecule_0_38 molecule_0_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 +molecule_0_38 molecule_0_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 +molecule_0_38 molecule_0_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 +molecule_0_38 molecule_0_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 +molecule_0_38 molecule_0_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 +molecule_0_38 molecule_0_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 +molecule_0_39 molecule_0_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 +molecule_0_39 molecule_0_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 +molecule_0_40 molecule_0_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 +molecule_0_40 molecule_0_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 +molecule_0_41 molecule_0_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 +molecule_0_42 molecule_0_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 +molecule_0_44 molecule_0_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 +molecule_0_49 molecule_0_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 +molecule_0_50 molecule_0_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 +molecule_0_50 molecule_0_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 +molecule_0_51 molecule_0_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 +molecule_0_51 molecule_0_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 +molecule_0_51 molecule_0_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 +molecule_0_51 molecule_0_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 +molecule_0_52 molecule_0_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 +molecule_0_52 molecule_0_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 +molecule_0_52 molecule_0_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 +molecule_0_53 molecule_0_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 +molecule_0_53 molecule_0_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 +molecule_0_54 molecule_0_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 +molecule_0_54 molecule_0_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 +molecule_0_54 molecule_0_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 +molecule_0_55 molecule_0_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 +molecule_0_55 molecule_0_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 +molecule_0_55 molecule_0_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 +molecule_0_55 molecule_0_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 +molecule_0_55 molecule_0_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 +molecule_0_55 molecule_0_38 1 0.53863592 9.41400000 ;go bond 0.6045983765957093 +molecule_0_55 molecule_0_39 1 0.46884965 9.41400000 ;go bond 0.5262659343028784 +molecule_0_55 molecule_0_40 1 0.49397051 9.41400000 ;go bond 0.5544631488965023 +molecule_0_56 molecule_0_31 1 0.63305577 9.41400000 ;go bond 0.7105810801311345 +molecule_0_56 molecule_0_32 1 0.57070473 9.41400000 ;go bond 0.6405943964432239 +molecule_0_56 molecule_0_35 1 0.54499611 9.41400000 ;go bond 0.6117374504966917 +molecule_0_57 molecule_0_35 1 0.59142457 9.41400000 ;go bond 0.6638516326030536 +molecule_0_57 molecule_0_36 1 0.73443635 9.41400000 ;go bond 0.8243769340599911 +molecule_0_57 molecule_0_42 1 0.68123116 9.41400000 ;go bond 0.7646561231921536 +molecule_0_57 molecule_0_43 1 0.72932038 9.41400000 ;go bond 0.8186344517277264 +molecule_0_57 molecule_0_44 1 0.71017360 9.41400000 ;go bond 0.7971429108051539 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molecule_0_50 1 0.65515556 9.41400000 ;go bond 0.7353872567523113 +molecule_0_63 molecule_0_58 1 0.62967119 9.41400000 ;go bond 0.7067820082223201 +molecule_0_63 molecule_0_59 1 0.46427561 9.41400000 ;go bond 0.521131754230626 +molecule_0_64 molecule_0_53 1 0.82959737 9.41400000 ;go bond 0.9311915604701376 +molecule_0_64 molecule_0_60 1 0.38156281 9.41400000 ;go bond 0.4282897748904594 +molecule_0_66 molecule_0_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 +molecule_0_66 molecule_0_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 +molecule_0_68 molecule_0_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 +molecule_0_69 molecule_0_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 +molecule_0_69 molecule_0_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 +molecule_0_69 molecule_0_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 +molecule_0_69 molecule_0_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 +molecule_0_70 molecule_0_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 +molecule_0_72 molecule_0_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 +molecule_0_72 molecule_0_61 1 0.44682674 9.41400000 ;go bond 0.5015460538054222 +molecule_0_72 molecule_0_64 1 0.62949829 9.41400000 ;go bond 0.7065879353028186 +molecule_0_73 molecule_0_61 1 0.53130673 9.41400000 ;go bond 0.5963716385459682 +molecule_0_73 molecule_0_62 1 0.40729971 9.41400000 ;go bond 0.4571784705977002 +molecule_0_74 molecule_0_62 1 0.44897571 9.41400000 ;go bond 0.5039581950921611 +molecule_0_74 molecule_0_63 1 0.38506256 9.41400000 ;go bond 0.43221810950469636 +molecule_0_74 molecule_0_64 1 0.43052761 9.41400000 ;go bond 0.4832509069633833 +molecule_0_74 molecule_0_65 1 0.61184241 9.41400000 ;go bond 0.6867698876930867 +molecule_0_75 molecule_0_62 1 0.52199782 9.41400000 ;go bond 0.5859227452973559 +molecule_0_75 molecule_0_63 1 0.40610455 9.41400000 ;go bond 0.45583694740556885 +molecule_0_76 molecule_0_63 1 0.46409225 9.41400000 ;go bond 0.5209259369461889 +molecule_0_78 molecule_0_63 1 0.57576077 9.41400000 ;go bond 0.6462696105707938 +molecule_0_78 molecule_0_64 1 0.45724502 9.41400000 ;go bond 0.5132401787770625 +molecule_0_78 molecule_0_65 1 0.43974215 9.41400000 ;go bond 0.4935938729629976 +molecule_0_78 molecule_0_74 1 0.56052614 9.41400000 ;go bond 0.6291693208239874 +molecule_0_79 molecule_0_64 1 0.52803406 9.41400000 ;go bond 0.5926981930678074 +molecule_0_79 molecule_0_65 1 0.39916015 9.41400000 ;go bond 0.44804212253596193 +molecule_0_80 molecule_0_53 1 0.60673469 9.41400000 ;go bond 0.6810366626079589 +molecule_0_80 molecule_0_60 1 0.73868742 9.41400000 ;go bond 0.8291485950674535 +molecule_0_80 molecule_0_64 1 0.54789421 9.41400000 ;go bond 0.6149904606975389 +molecule_0_80 molecule_0_65 1 0.47057069 9.41400000 ;go bond 0.5281977457102484 +molecule_0_80 molecule_0_66 1 0.58883652 9.41400000 ;go bond 0.6609466408239479 +molecule_0_82 molecule_0_78 1 0.66632073 9.41400000 ;go bond 0.7479197331826131 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1 0.64785523 9.41400000 ;go bond 0.7271929039256984 +molecule_0_86 molecule_0_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 +molecule_0_86 molecule_0_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 +molecule_0_86 molecule_0_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 +molecule_0_88 molecule_0_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 +molecule_0_88 molecule_0_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 +molecule_0_88 molecule_0_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 +molecule_0_88 molecule_0_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 +molecule_0_88 molecule_0_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 +molecule_0_88 molecule_0_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 +molecule_0_89 molecule_0_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 +molecule_0_89 molecule_0_15 1 0.69215886 9.41400000 ;go bond 0.7769220558398894 +molecule_0_90 molecule_0_78 1 0.80563795 9.41400000 ;go bond 0.9042980239792853 +molecule_0_90 molecule_0_82 1 0.59740893 9.41400000 ;go bond 0.6705688513824994 +molecule_0_90 molecule_0_83 1 0.57714934 9.41400000 ;go bond 0.6478282257424317 +molecule_0_91 molecule_0_55 1 0.70847337 9.41400000 ;go bond 0.7952344695348353 +molecule_0_91 molecule_0_58 1 0.76773720 9.41400000 ;go bond 0.8617558647944001 +molecule_0_91 molecule_0_83 1 0.57795007 9.41400000 ;go bond 0.6487270215620753 +molecule_0_92 molecule_0_15 1 0.66057405 9.41400000 ;go bond 0.741469302181026 +molecule_0_92 molecule_0_17 1 0.76276340 9.41400000 ;go bond 0.8561729710147924 +molecule_0_92 molecule_0_88 1 0.55891711 9.41400000 ;go bond 0.6273632448163519 +molecule_0_93 molecule_0_89 1 0.55091233 9.41400000 ;go bond 0.6183781864423775 +molecule_0_94 molecule_0_58 1 0.80192436 9.41400000 ;go bond 0.9001296640477775 +molecule_0_94 molecule_0_63 1 0.69400655 9.41400000 ;go bond 0.7789960144450432 +molecule_0_94 molecule_0_76 1 0.58706169 9.41400000 ;go bond 0.6589544684537765 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1 0.84557275 9.41400000 ;go bond 0.9491233248865086 +molecule_0_97 molecule_0_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 +molecule_0_97 molecule_0_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 +molecule_0_98 molecule_0_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 +molecule_0_98 molecule_0_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 +molecule_0_98 molecule_0_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 +molecule_0_99 molecule_0_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 +molecule_0_99 molecule_0_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 +molecule_0_99 molecule_0_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 +molecule_0_99 molecule_0_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 +molecule_0_100 molecule_0_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 +molecule_0_100 molecule_0_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 +molecule_0_100 molecule_0_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 +molecule_0_101 molecule_0_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 +molecule_0_104 molecule_0_23 1 0.90496194 9.41400000 ;go bond 1.0157854279713863 +molecule_0_104 molecule_0_99 1 0.37779975 9.41400000 ;go bond 0.42406587714866395 +molecule_0_105 molecule_0_23 1 0.85792539 9.41400000 ;go bond 0.9629886926477136 +molecule_0_105 molecule_0_27 1 0.80028132 9.41400000 ;go bond 0.8982854095190085 +molecule_0_105 molecule_0_28 1 0.85914649 9.41400000 ;go bond 0.9643593287596212 +molecule_0_105 molecule_0_31 1 0.84674626 9.41400000 ;go bond 0.950440544780807 +molecule_0_105 molecule_0_99 1 0.58741430 9.41400000 ;go bond 0.6593502594081683 +molecule_0_107 molecule_0_98 1 0.70183885 9.41400000 ;go bond 0.7877874714268905 +molecule_0_108 molecule_0_28 1 0.92956079 9.41400000 ;go bond 1.0433967044744268 +molecule_0_108 molecule_0_35 1 0.82960839 9.41400000 ;go bond 0.9312039368635526 +molecule_0_108 molecule_0_56 1 0.78133210 9.41400000 ;go bond 0.8770156294387439 +molecule_0_108 molecule_0_57 1 0.77168204 9.41400000 ;go bond 0.8661838041857776 +molecule_0_108 molecule_0_98 1 0.90403083 9.41400000 ;go bond 1.014740292066367 +molecule_0_108 molecule_0_99 1 0.90315750 9.41400000 ;go bond 1.0137600206889819 +molecule_0_110 molecule_0_34 1 0.54869664 9.41400000 ;go bond 0.6158911542488904 +molecule_0_110 molecule_0_35 1 0.64980269 9.41400000 ;go bond 0.7293788607697123 +molecule_0_111 molecule_0_27 1 0.70311941 9.41400000 ;go bond 0.7892248529963473 +molecule_0_111 molecule_0_31 1 0.56259884 9.41400000 ;go bond 0.6314958500157425 +molecule_0_111 molecule_0_105 1 0.59346888 9.41400000 ;go bond 0.6661462995266982 +molecule_0_111 molecule_0_106 1 0.59882239 9.41400000 ;go bond 0.6721554100763635 +molecule_0_112 molecule_0_106 1 0.57753815 9.41400000 ;go bond 0.6482646568405853 +molecule_0_112 molecule_0_107 1 0.74260248 9.41400000 ;go bond 0.833543103918769 +molecule_0_112 molecule_0_108 1 0.53753958 9.41400000 ;go bond 0.603367775987529 +molecule_0_113 molecule_0_109 1 0.53306219 9.41400000 ;go bond 0.5983420831461288 +molecule_0_114 molecule_0_34 1 0.72771145 9.41400000 ;go bond 0.8168284821715603 +molecule_0_114 molecule_0_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 +molecule_0_115 molecule_0_30 1 0.62277169 9.41400000 ;go bond 0.6990375917289473 +molecule_0_115 molecule_0_31 1 0.71820218 9.41400000 ;go bond 0.8061546928175227 +molecule_0_115 molecule_0_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 +molecule_0_115 molecule_0_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 +molecule_0_115 molecule_0_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 +molecule_0_116 molecule_0_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 +molecule_0_116 molecule_0_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 +molecule_0_116 molecule_0_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 +molecule_0_118 molecule_0_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 +molecule_0_120 molecule_0_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 +molecule_0_120 molecule_0_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 +molecule_0_120 molecule_0_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 +molecule_0_120 molecule_0_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 +molecule_0_120 molecule_0_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 +molecule_0_122 molecule_0_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 +molecule_0_123 molecule_0_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 +molecule_0_123 molecule_0_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 +molecule_0_123 molecule_0_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 +molecule_0_123 molecule_0_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 +molecule_0_123 molecule_0_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 +molecule_0_123 molecule_0_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 +molecule_0_124 molecule_0_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 +molecule_0_124 molecule_0_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 +molecule_0_124 molecule_0_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 +molecule_0_124 molecule_0_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 +molecule_0_124 molecule_0_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 +molecule_0_125 molecule_0_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 +molecule_0_125 molecule_0_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 +molecule_0_127 molecule_0_5 1 0.79805432 9.41400000 ;go bond 0.8957856911439042 +molecule_0_127 molecule_0_6 1 0.59870073 9.41400000 ;go bond 0.6720188457372778 +molecule_0_129 molecule_0_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 +molecule_0_129 molecule_0_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 +molecule_0_129 molecule_0_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 +molecule_0_129 molecule_0_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 +W molecule_0_1 1 0.47000000 1.00000000 ;water bias C +W molecule_0_2 1 0.41000000 -0.50000000 ;water bias E +W molecule_0_3 1 0.47000000 1.00000000 ;water bias C +W molecule_0_4 1 0.41000000 1.00000000 ;water bias C +W molecule_0_9 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_10 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_17 1 0.47000000 1.00000000 ;water bias C +W molecule_0_20 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_23 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_24 1 0.47000000 1.00000000 ;water bias C +W molecule_0_29 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_30 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_31 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_32 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_39 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_42 1 0.41000000 1.00000000 ;water bias C +W molecule_0_43 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_44 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_45 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_46 1 0.47000000 1.00000000 ;water bias C +W molecule_0_50 1 0.47000000 1.00000000 ;water bias C +W molecule_0_51 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_52 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_53 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_58 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_59 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_64 1 0.47000000 1.00000000 ;water bias C +W molecule_0_65 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_66 1 0.47000000 1.00000000 ;water bias C +W molecule_0_68 1 0.47000000 1.00000000 ;water bias C +W molecule_0_69 1 0.47000000 1.00000000 ;water bias C +W molecule_0_72 1 0.47000000 1.00000000 ;water bias C +W molecule_0_73 1 0.47000000 1.00000000 ;water bias C +W molecule_0_74 1 0.47000000 1.00000000 ;water bias C +W molecule_0_77 1 0.47000000 1.00000000 ;water bias C +W molecule_0_79 1 0.41000000 -0.50000000 ;water bias E +W molecule_0_88 1 0.47000000 1.00000000 ;water bias C +W molecule_0_93 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_94 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_95 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_96 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_119 1 0.47000000 1.00000000 ;water bias C +W molecule_0_127 1 0.47000000 1.00000000 ;water bias C +W molecule_0_128 1 0.47000000 1.00000000 ;water bias C +W molecule_0_129 1 0.47000000 1.00000000 ;water bias C diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule.itp deleted file mode 100644 index 4322ae056..000000000 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule.itp +++ /dev/null @@ -1,2027 +0,0 @@ -; This file was generated using the following command: -; /coarse/chris/python_packages/vermouth_dev/vermouth-martinize/venv/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go ../map.map -water-bias -water-bias-eps E:-.5 C:1.0 H:-1.0 -; martinize with vermouth 0.0.1.dev1783 -; The following sequence of secondary structure -; was used for the full system: -; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC - -; Please cite the following papers: -; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 -; Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; 2024; 10.1101/2024.04.15.589479 - -[ moleculetype ] -molecule 1 - -[ atoms ] - 1 Q5 1 LYS BB 1 1 - 2 SC3 1 LYS SC1 2 0.0 - 3 SQ4p 1 LYS SC2 3 1.0 - 4 SP2 2 VAL BB 4 0.0 - 5 SC3 2 VAL SC1 5 0.0 - 6 P2 3 PHE BB 6 0.0 - 7 SC4 3 PHE SC1 7 0.0 - 8 TC5 3 PHE SC2 8 0.0 - 9 TC5 3 PHE SC3 9 0.0 - 10 SP1 4 GLY BB 10 0.0 - 11 P2 5 ARG BB 11 0.0 - 12 SC3 5 ARG SC1 12 0.0 - 13 SQ3p 5 ARG SC2 13 1.0 - 14 P2 6 CYS BB 14 0.0 - 15 TC6 6 CYS SC1 15 0.0 - 16 P2 7 GLU BB 16 0.0 - 17 Q5n 7 GLU SC1 17 -1.0 - 18 P2 8 LEU BB 18 0.0 - 19 SC2 8 LEU SC1 19 0.0 - 20 SP2 9 ALA BB 20 0.0 - 21 TC3 9 ALA SC1 21 0.0 - 22 SP2 10 ALA BB 22 0.0 - 23 TC3 10 ALA SC1 23 0.0 - 24 SP2 11 ALA BB 24 0.0 - 25 TC3 11 ALA SC1 25 0.0 - 26 P2 12 MET BB 26 0.0 - 27 C6 12 MET SC1 27 0.0 - 28 P2 13 LYS BB 28 0.0 - 29 SC3 13 LYS SC1 29 0.0 - 30 SQ4p 13 LYS SC2 30 1.0 - 31 P2 14 ARG BB 31 0.0 - 32 SC3 14 ARG SC1 32 0.0 - 33 SQ3p 14 ARG SC2 33 1.0 - 34 P2 15 HIS BB 34 0.0 - 35 TC4 15 HIS SC1 35 0.0 - 36 TN6d 15 HIS SC2 36 0.0 - 37 TN5a 15 HIS SC3 37 0.0 - 38 SP1 16 GLY BB 38 0.0 - 39 P2 17 LEU BB 39 0.0 - 40 SC2 17 LEU SC1 40 0.0 - 41 P2 18 ASP BB 41 0.0 - 42 SQ5n 18 ASP SC1 42 -1.0 - 43 P2 19 ASN BB 43 0.0 - 44 SP5 19 ASN SC1 44 0.0 - 45 P2 20 TYR BB 45 0.0 - 46 TC4 20 TYR SC1 46 0.0 - 47 TC5 20 TYR SC2 47 0.0 - 48 TC5 20 TYR SC3 48 0.0 - 49 TN6 20 TYR SC4 49 0.0 - 50 P2 21 ARG BB 50 0.0 - 51 SC3 21 ARG SC1 51 0.0 - 52 SQ3p 21 ARG SC2 52 1.0 - 53 SP1 22 GLY BB 53 0.0 - 54 P2 23 TYR BB 54 0.0 - 55 TC4 23 TYR SC1 55 0.0 - 56 TC5 23 TYR SC2 56 0.0 - 57 TC5 23 TYR SC3 57 0.0 - 58 TN6 23 TYR SC4 58 0.0 - 59 P2 24 SER BB 59 0.0 - 60 TP1 24 SER SC1 60 0.0 - 61 P2 25 LEU BB 61 0.0 - 62 SC2 25 LEU SC1 62 0.0 - 63 SP1 26 GLY BB 63 0.0 - 64 P2 27 ASN BB 64 0.0 - 65 SP5 27 ASN SC1 65 0.0 - 66 P2 28 TRP BB 66 0.0 - 67 TC4 28 TRP SC1 67 0.0 36.0 - 68 TN6d 28 TRP SC2 68 0.0 36.0 - 69 TC5 28 TRP SC3 69 0.0 0.0 - 70 TC5 28 TRP SC4 70 0.0 36.0 - 71 TC5 28 TRP SC5 71 0.0 36.0 - 72 SP2 29 VAL BB 72 0.0 - 73 SC3 29 VAL SC1 73 0.0 - 74 P2 30 CYS BB 74 0.0 - 75 TC6 30 CYS SC1 75 0.0 - 76 SP2 31 ALA BB 76 0.0 - 77 TC3 31 ALA SC1 77 0.0 - 78 SP2 32 ALA BB 78 0.0 - 79 TC3 32 ALA SC1 79 0.0 - 80 P2 33 LYS BB 80 0.0 - 81 SC3 33 LYS SC1 81 0.0 - 82 SQ4p 33 LYS SC2 82 1.0 - 83 P2 34 PHE BB 83 0.0 - 84 SC4 34 PHE SC1 84 0.0 - 85 TC5 34 PHE SC2 85 0.0 - 86 TC5 34 PHE SC3 86 0.0 - 87 P2 35 GLU BB 87 0.0 - 88 Q5n 35 GLU SC1 88 -1.0 - 89 P2 36 SER BB 89 0.0 - 90 TP1 36 SER SC1 90 0.0 - 91 P2 37 ASN BB 91 0.0 - 92 SP5 37 ASN SC1 92 0.0 - 93 P2 38 PHE BB 93 0.0 - 94 SC4 38 PHE SC1 94 0.0 - 95 TC5 38 PHE SC2 95 0.0 - 96 TC5 38 PHE SC3 96 0.0 - 97 P2 39 ASN BB 97 0.0 - 98 SP5 39 ASN SC1 98 0.0 - 99 P2 40 THR BB 99 0.0 -100 SP1 40 THR SC1 100 0.0 -101 P2 41 GLN BB 101 0.0 -102 P5 41 GLN SC1 102 0.0 -103 SP2 42 ALA BB 103 0.0 -104 TC3 42 ALA SC1 104 0.0 -105 P2 43 THR BB 105 0.0 -106 SP1 43 THR SC1 106 0.0 -107 P2 44 ASN BB 107 0.0 -108 SP5 44 ASN SC1 108 0.0 -109 P2 45 ARG BB 109 0.0 -110 SC3 45 ARG SC1 110 0.0 -111 SQ3p 45 ARG SC2 111 1.0 -112 P2 46 ASN BB 112 0.0 -113 SP5 46 ASN SC1 113 0.0 -114 P2 47 THR BB 114 0.0 -115 SP1 47 THR SC1 115 0.0 -116 P2 48 ASP BB 116 0.0 -117 SQ5n 48 ASP SC1 117 -1.0 -118 SP1 49 GLY BB 118 0.0 -119 P2 50 SER BB 119 0.0 -120 TP1 50 SER SC1 120 0.0 -121 P2 51 THR BB 121 0.0 -122 SP1 51 THR SC1 122 0.0 -123 P2 52 ASP BB 123 0.0 -124 SQ5n 52 ASP SC1 124 -1.0 -125 P2 53 TYR BB 125 0.0 -126 TC4 53 TYR SC1 126 0.0 -127 TC5 53 TYR SC2 127 0.0 -128 TC5 53 TYR SC3 128 0.0 -129 TN6 53 TYR SC4 129 0.0 -130 SP1 54 GLY BB 130 0.0 -131 P2 55 ILE BB 131 0.0 -132 SC2 55 ILE SC1 132 0.0 -133 P2 56 LEU BB 133 0.0 -134 SC2 56 LEU SC1 134 0.0 -135 P2 57 GLN BB 135 0.0 -136 P5 57 GLN SC1 136 0.0 -137 P2 58 ILE BB 137 0.0 -138 SC2 58 ILE SC1 138 0.0 -139 P2 59 ASN BB 139 0.0 -140 SP5 59 ASN SC1 140 0.0 -141 P2 60 SER BB 141 0.0 -142 TP1 60 SER SC1 142 0.0 -143 P2 61 ARG BB 143 0.0 -144 SC3 61 ARG SC1 144 0.0 -145 SQ3p 61 ARG SC2 145 1.0 -146 P2 62 TRP BB 146 0.0 -147 TC4 62 TRP SC1 147 0.0 36.0 -148 TN6d 62 TRP SC2 148 0.0 36.0 -149 TC5 62 TRP SC3 149 0.0 0.0 -150 TC5 62 TRP SC4 150 0.0 36.0 -151 TC5 62 TRP SC5 151 0.0 36.0 -152 P2 63 TRP BB 152 0.0 -153 TC4 63 TRP SC1 153 0.0 36.0 -154 TN6d 63 TRP SC2 154 0.0 36.0 -155 TC5 63 TRP SC3 155 0.0 0.0 -156 TC5 63 TRP SC4 156 0.0 36.0 -157 TC5 63 TRP SC5 157 0.0 36.0 -158 P2 64 CYS BB 158 0.0 -159 TC6 64 CYS SC1 159 0.0 -160 P2 65 ASN BB 160 0.0 -161 SP5 65 ASN SC1 161 0.0 -162 P2 66 ASP BB 162 0.0 -163 SQ5n 66 ASP SC1 163 -1.0 -164 SP1 67 GLY BB 164 0.0 -165 P2 68 ARG BB 165 0.0 -166 SC3 68 ARG SC1 166 0.0 -167 SQ3p 68 ARG SC2 167 1.0 -168 P2 69 THR BB 168 0.0 -169 SP1 69 THR SC1 169 0.0 -170 SP2a 70 PRO BB 170 0.0 -171 SC3 70 PRO SC1 171 0.0 -172 SP1 71 GLY BB 172 0.0 -173 P2 72 SER BB 173 0.0 -174 TP1 72 SER SC1 174 0.0 -175 P2 73 ARG BB 175 0.0 -176 SC3 73 ARG SC1 176 0.0 -177 SQ3p 73 ARG SC2 177 1.0 -178 P2 74 ASN BB 178 0.0 -179 SP5 74 ASN SC1 179 0.0 -180 P2 75 LEU BB 180 0.0 -181 SC2 75 LEU SC1 181 0.0 -182 P2 76 CYS BB 182 0.0 -183 TC6 76 CYS SC1 183 0.0 -184 P2 77 ASN BB 184 0.0 -185 SP5 77 ASN SC1 185 0.0 -186 P2 78 ILE BB 186 0.0 -187 SC2 78 ILE SC1 187 0.0 -188 SP2a 79 PRO BB 188 0.0 -189 SC3 79 PRO SC1 189 0.0 -190 P2 80 CYS BB 190 0.0 -191 TC6 80 CYS SC1 191 0.0 -192 P2 81 SER BB 192 0.0 -193 TP1 81 SER SC1 193 0.0 -194 SP2 82 ALA BB 194 0.0 -195 TC3 82 ALA SC1 195 0.0 -196 P2 83 LEU BB 196 0.0 -197 SC2 83 LEU SC1 197 0.0 -198 P2 84 LEU BB 198 0.0 -199 SC2 84 LEU SC1 199 0.0 -200 P2 85 SER BB 200 0.0 -201 TP1 85 SER SC1 201 0.0 -202 P2 86 SER BB 202 0.0 -203 TP1 86 SER SC1 203 0.0 -204 P2 87 ASP BB 204 0.0 -205 SQ5n 87 ASP SC1 205 -1.0 -206 P2 88 ILE BB 206 0.0 -207 SC2 88 ILE SC1 207 0.0 -208 P2 89 THR BB 208 0.0 -209 SP1 89 THR SC1 209 0.0 -210 SP2 90 ALA BB 210 0.0 -211 TC3 90 ALA SC1 211 0.0 -212 P2 91 SER BB 212 0.0 -213 TP1 91 SER SC1 213 0.0 -214 SP2 92 VAL BB 214 0.0 -215 SC3 92 VAL SC1 215 0.0 -216 P2 93 ASN BB 216 0.0 -217 SP5 93 ASN SC1 217 0.0 -218 P2 94 CYS BB 218 0.0 -219 TC6 94 CYS SC1 219 0.0 -220 SP2 95 ALA BB 220 0.0 -221 TC3 95 ALA SC1 221 0.0 -222 P2 96 LYS BB 222 0.0 -223 SC3 96 LYS SC1 223 0.0 -224 SQ4p 96 LYS SC2 224 1.0 -225 P2 97 LYS BB 225 0.0 -226 SC3 97 LYS SC1 226 0.0 -227 SQ4p 97 LYS SC2 227 1.0 -228 P2 98 ILE BB 228 0.0 -229 SC2 98 ILE SC1 229 0.0 -230 SP2 99 VAL BB 230 0.0 -231 SC3 99 VAL SC1 231 0.0 -232 P2 100 SER BB 232 0.0 -233 TP1 100 SER SC1 233 0.0 -234 P2 101 ASP BB 234 0.0 -235 SQ5n 101 ASP SC1 235 -1.0 -236 SP1 102 GLY BB 236 0.0 -237 P2 103 ASN BB 237 0.0 -238 SP5 103 ASN SC1 238 0.0 -239 SP1 104 GLY BB 239 0.0 -240 P2 105 MET BB 240 0.0 -241 C6 105 MET SC1 241 0.0 -242 P2 106 ASN BB 242 0.0 -243 SP5 106 ASN SC1 243 0.0 -244 SP2 107 ALA BB 244 0.0 -245 TC3 107 ALA SC1 245 0.0 -246 P2 108 TRP BB 246 0.0 -247 TC4 108 TRP SC1 247 0.0 36.0 -248 TN6d 108 TRP SC2 248 0.0 36.0 -249 TC5 108 TRP SC3 249 0.0 0.0 -250 TC5 108 TRP SC4 250 0.0 36.0 -251 TC5 108 TRP SC5 251 0.0 36.0 -252 SP2 109 VAL BB 252 0.0 -253 SC3 109 VAL SC1 253 0.0 -254 SP2 110 ALA BB 254 0.0 -255 TC3 110 ALA SC1 255 0.0 -256 P2 111 TRP BB 256 0.0 -257 TC4 111 TRP SC1 257 0.0 36.0 -258 TN6d 111 TRP SC2 258 0.0 36.0 -259 TC5 111 TRP SC3 259 0.0 0.0 -260 TC5 111 TRP SC4 260 0.0 36.0 -261 TC5 111 TRP SC5 261 0.0 36.0 -262 P2 112 ARG BB 262 0.0 -263 SC3 112 ARG SC1 263 0.0 -264 SQ3p 112 ARG SC2 264 1.0 -265 P2 113 ASN BB 265 0.0 -266 SP5 113 ASN SC1 266 0.0 -267 P2 114 ARG BB 267 0.0 -268 SC3 114 ARG SC1 268 0.0 -269 SQ3p 114 ARG SC2 269 1.0 -270 P2 115 CYS BB 270 0.0 -271 TC6 115 CYS SC1 271 0.0 -272 P2 116 LYS BB 272 0.0 -273 SC3 116 LYS SC1 273 0.0 -274 SQ4p 116 LYS SC2 274 1.0 -275 SP1 117 GLY BB 275 0.0 -276 P2 118 THR BB 276 0.0 -277 SP1 118 THR SC1 277 0.0 -278 P2 119 ASP BB 278 0.0 -279 SQ5n 119 ASP SC1 279 -1.0 -280 SP2 120 VAL BB 280 0.0 -281 SC3 120 VAL SC1 281 0.0 -282 P2 121 GLN BB 282 0.0 -283 P5 121 GLN SC1 283 0.0 -284 SP2 122 ALA BB 284 0.0 -285 TC3 122 ALA SC1 285 0.0 -286 P2 123 TRP BB 286 0.0 -287 TC4 123 TRP SC1 287 0.0 36.0 -288 TN6d 123 TRP SC2 288 0.0 36.0 -289 TC5 123 TRP SC3 289 0.0 0.0 -290 TC5 123 TRP SC4 290 0.0 36.0 -291 TC5 123 TRP SC5 291 0.0 36.0 -292 P2 124 ILE BB 292 0.0 -293 SC2 124 ILE SC1 293 0.0 -294 P2 125 ARG BB 294 0.0 -295 SC3 125 ARG SC1 295 0.0 -296 SQ3p 125 ARG SC2 296 1.0 -297 SP1 126 GLY BB 297 0.0 -298 P2 127 CYS BB 298 0.0 -299 TC6 127 CYS SC1 299 0.0 -300 P2 128 ARG BB 300 0.0 -301 SC3 128 ARG SC1 301 0.0 -302 SQ3p 128 ARG SC2 302 1.0 -303 Q5 129 LEU BB 303 -1 -304 SC2 129 LEU SC1 304 0.0 -305 molecule_1 1 LYS CA 305 0 0.0 -306 molecule_2 2 VAL CA 306 0 0.0 -307 molecule_3 3 PHE CA 307 0 0.0 -308 molecule_4 4 GLY CA 308 0 0.0 -309 molecule_5 5 ARG CA 309 0 0.0 -310 molecule_6 6 CYS CA 310 0 0.0 -311 molecule_7 7 GLU CA 311 0 0.0 -312 molecule_8 8 LEU CA 312 0 0.0 -313 molecule_9 9 ALA CA 313 0 0.0 -314 molecule_10 10 ALA CA 314 0 0.0 -315 molecule_11 11 ALA CA 315 0 0.0 -316 molecule_12 12 MET CA 316 0 0.0 -317 molecule_13 13 LYS CA 317 0 0.0 -318 molecule_14 14 ARG CA 318 0 0.0 -319 molecule_15 15 HIS CA 319 0 0.0 -320 molecule_16 16 GLY CA 320 0 0.0 -321 molecule_17 17 LEU CA 321 0 0.0 -322 molecule_18 18 ASP CA 322 0 0.0 -323 molecule_19 19 ASN CA 323 0 0.0 -324 molecule_20 20 TYR CA 324 0 0.0 -325 molecule_21 21 ARG CA 325 0 0.0 -326 molecule_22 22 GLY CA 326 0 0.0 -327 molecule_23 23 TYR CA 327 0 0.0 -328 molecule_24 24 SER CA 328 0 0.0 -329 molecule_25 25 LEU CA 329 0 0.0 -330 molecule_26 26 GLY CA 330 0 0.0 -331 molecule_27 27 ASN CA 331 0 0.0 -332 molecule_28 28 TRP CA 332 0 0.0 -333 molecule_29 29 VAL CA 333 0 0.0 -334 molecule_30 30 CYS CA 334 0 0.0 -335 molecule_31 31 ALA CA 335 0 0.0 -336 molecule_32 32 ALA CA 336 0 0.0 -337 molecule_33 33 LYS CA 337 0 0.0 -338 molecule_34 34 PHE CA 338 0 0.0 -339 molecule_35 35 GLU CA 339 0 0.0 -340 molecule_36 36 SER CA 340 0 0.0 -341 molecule_37 37 ASN CA 341 0 0.0 -342 molecule_38 38 PHE CA 342 0 0.0 -343 molecule_39 39 ASN CA 343 0 0.0 -344 molecule_40 40 THR CA 344 0 0.0 -345 molecule_41 41 GLN CA 345 0 0.0 -346 molecule_42 42 ALA CA 346 0 0.0 -347 molecule_43 43 THR CA 347 0 0.0 -348 molecule_44 44 ASN CA 348 0 0.0 -349 molecule_45 45 ARG CA 349 0 0.0 -350 molecule_46 46 ASN CA 350 0 0.0 -351 molecule_47 47 THR CA 351 0 0.0 -352 molecule_48 48 ASP CA 352 0 0.0 -353 molecule_49 49 GLY CA 353 0 0.0 -354 molecule_50 50 SER CA 354 0 0.0 -355 molecule_51 51 THR CA 355 0 0.0 -356 molecule_52 52 ASP CA 356 0 0.0 -357 molecule_53 53 TYR CA 357 0 0.0 -358 molecule_54 54 GLY CA 358 0 0.0 -359 molecule_55 55 ILE CA 359 0 0.0 -360 molecule_56 56 LEU CA 360 0 0.0 -361 molecule_57 57 GLN CA 361 0 0.0 -362 molecule_58 58 ILE CA 362 0 0.0 -363 molecule_59 59 ASN CA 363 0 0.0 -364 molecule_60 60 SER CA 364 0 0.0 -365 molecule_61 61 ARG CA 365 0 0.0 -366 molecule_62 62 TRP CA 366 0 0.0 -367 molecule_63 63 TRP CA 367 0 0.0 -368 molecule_64 64 CYS CA 368 0 0.0 -369 molecule_65 65 ASN CA 369 0 0.0 -370 molecule_66 66 ASP CA 370 0 0.0 -371 molecule_67 67 GLY CA 371 0 0.0 -372 molecule_68 68 ARG CA 372 0 0.0 -373 molecule_69 69 THR CA 373 0 0.0 -374 molecule_70 70 PRO CA 374 0 0.0 -375 molecule_71 71 GLY CA 375 0 0.0 -376 molecule_72 72 SER CA 376 0 0.0 -377 molecule_73 73 ARG CA 377 0 0.0 -378 molecule_74 74 ASN CA 378 0 0.0 -379 molecule_75 75 LEU CA 379 0 0.0 -380 molecule_76 76 CYS CA 380 0 0.0 -381 molecule_77 77 ASN CA 381 0 0.0 -382 molecule_78 78 ILE CA 382 0 0.0 -383 molecule_79 79 PRO CA 383 0 0.0 -384 molecule_80 80 CYS CA 384 0 0.0 -385 molecule_81 81 SER CA 385 0 0.0 -386 molecule_82 82 ALA CA 386 0 0.0 -387 molecule_83 83 LEU CA 387 0 0.0 -388 molecule_84 84 LEU CA 388 0 0.0 -389 molecule_85 85 SER CA 389 0 0.0 -390 molecule_86 86 SER CA 390 0 0.0 -391 molecule_87 87 ASP CA 391 0 0.0 -392 molecule_88 88 ILE CA 392 0 0.0 -393 molecule_89 89 THR CA 393 0 0.0 -394 molecule_90 90 ALA CA 394 0 0.0 -395 molecule_91 91 SER CA 395 0 0.0 -396 molecule_92 92 VAL CA 396 0 0.0 -397 molecule_93 93 ASN CA 397 0 0.0 -398 molecule_94 94 CYS CA 398 0 0.0 -399 molecule_95 95 ALA CA 399 0 0.0 -400 molecule_96 96 LYS CA 400 0 0.0 -401 molecule_97 97 LYS CA 401 0 0.0 -402 molecule_98 98 ILE CA 402 0 0.0 -403 molecule_99 99 VAL CA 403 0 0.0 -404 molecule_100 100 SER CA 404 0 0.0 -405 molecule_101 101 ASP CA 405 0 0.0 -406 molecule_102 102 GLY CA 406 0 0.0 -407 molecule_103 103 ASN CA 407 0 0.0 -408 molecule_104 104 GLY CA 408 0 0.0 -409 molecule_105 105 MET CA 409 0 0.0 -410 molecule_106 106 ASN CA 410 0 0.0 -411 molecule_107 107 ALA CA 411 0 0.0 -412 molecule_108 108 TRP CA 412 0 0.0 -413 molecule_109 109 VAL CA 413 0 0.0 -414 molecule_110 110 ALA CA 414 0 0.0 -415 molecule_111 111 TRP CA 415 0 0.0 -416 molecule_112 112 ARG CA 416 0 0.0 -417 molecule_113 113 ASN CA 417 0 0.0 -418 molecule_114 114 ARG CA 418 0 0.0 -419 molecule_115 115 CYS CA 419 0 0.0 -420 molecule_116 116 LYS CA 420 0 0.0 -421 molecule_117 117 GLY CA 421 0 0.0 -422 molecule_118 118 THR CA 422 0 0.0 -423 molecule_119 119 ASP CA 423 0 0.0 -424 molecule_120 120 VAL CA 424 0 0.0 -425 molecule_121 121 GLN CA 425 0 0.0 -426 molecule_122 122 ALA CA 426 0 0.0 -427 molecule_123 123 TRP CA 427 0 0.0 -428 molecule_124 124 ILE CA 428 0 0.0 -429 molecule_125 125 ARG CA 429 0 0.0 -430 molecule_126 126 GLY CA 430 0 0.0 -431 molecule_127 127 CYS CA 431 0 0.0 -432 molecule_128 128 ARG CA 432 0 0.0 -433 molecule_129 129 LEU CA 433 0 0.0 - -[ bonds ] -; Backbone bonds - 1 4 1 0.350 4000 - 4 6 1 0.350 4000 - 6 10 1 0.350 4000 - 34 38 1 0.350 4000 - 38 39 1 0.350 4000 - 39 41 1 0.350 4000 - 41 43 1 0.350 4000 - 43 45 1 0.350 4000 - 45 50 1 0.350 4000 - 50 53 1 0.350 4000 - 53 54 1 0.350 4000 - 54 59 1 0.350 4000 - 91 93 1 0.350 4000 - 93 97 1 0.350 4000 - 97 99 1 0.350 4000 - 99 101 1 0.350 4000 -101 103 1 0.350 4000 -103 105 1 0.350 4000 -105 107 1 0.350 4000 -107 109 1 0.350 4000 -109 112 1 0.350 4000 -112 114 1 0.350 4000 -114 116 1 0.350 4000 -116 118 1 0.350 4000 -118 119 1 0.350 4000 -119 121 1 0.350 4000 -121 123 1 0.350 4000 -123 125 1 0.350 4000 -125 130 1 0.350 4000 -130 131 1 0.350 4000 -131 133 1 0.350 4000 -133 135 1 0.350 4000 -135 137 1 0.350 4000 -137 139 1 0.350 4000 -139 141 1 0.350 4000 -141 143 1 0.350 4000 -143 146 1 0.350 4000 -146 152 1 0.350 4000 -152 158 1 0.350 4000 -158 160 1 0.350 4000 -160 162 1 0.350 4000 -162 164 1 0.350 4000 -164 165 1 0.350 4000 -165 168 1 0.350 4000 -168 170 1 0.350 4000 -170 172 1 0.350 4000 -172 173 1 0.350 4000 -173 175 1 0.350 4000 -175 178 1 0.350 4000 -178 180 1 0.350 4000 -180 182 1 0.350 4000 -182 184 1 0.350 4000 -184 186 1 0.350 4000 -186 188 1 0.350 4000 -200 202 1 0.350 4000 -202 204 1 0.350 4000 -204 206 1 0.350 4000 -234 236 1 0.350 4000 -236 237 1 0.350 4000 -270 272 1 0.350 4000 -272 275 1 0.350 4000 -275 276 1 0.350 4000 -276 278 1 0.350 4000 -294 297 1 0.350 4000 -297 298 1 0.350 4000 -298 300 1 0.350 4000 -300 303 1 0.350 4000 - -; Side chain bonds - 1 2 1 0.330 5000 - 2 3 1 0.360 5000 - 6 7 1 0.325 7500 - 11 12 1 0.330 5000 - 12 13 1 0.380 5000 - 14 15 1 0.341 7500 - 16 17 1 0.400 5000 - 18 19 1 0.363 7500 - 26 27 1 0.40 2500 - 28 29 1 0.330 5000 - 29 30 1 0.360 5000 - 31 32 1 0.330 5000 - 32 33 1 0.380 5000 - 34 35 1 0.336 7500 - 39 40 1 0.363 7500 - 41 42 1 0.352 7500 - 43 44 1 0.352 5000 - 45 46 1 0.325 5000 - 50 51 1 0.330 5000 - 51 52 1 0.380 5000 - 54 55 1 0.325 5000 - 59 60 1 0.287 7500 - 61 62 1 0.363 7500 - 64 65 1 0.352 5000 - 66 67 1 0.315 5000 - 74 75 1 0.341 7500 - 80 81 1 0.330 5000 - 81 82 1 0.360 5000 - 83 84 1 0.325 7500 - 87 88 1 0.400 5000 - 89 90 1 0.287 7500 - 91 92 1 0.352 5000 - 93 94 1 0.325 7500 - 97 98 1 0.352 5000 -101 102 1 0.400 5000 -107 108 1 0.352 5000 -109 110 1 0.330 5000 -110 111 1 0.380 5000 -112 113 1 0.352 5000 -116 117 1 0.352 7500 -119 120 1 0.287 7500 -123 124 1 0.352 7500 -125 126 1 0.325 5000 -133 134 1 0.363 7500 -135 136 1 0.400 5000 -139 140 1 0.352 5000 -141 142 1 0.287 7500 -143 144 1 0.330 5000 -144 145 1 0.380 5000 -146 147 1 0.315 5000 -152 153 1 0.315 5000 -158 159 1 0.341 7500 -160 161 1 0.352 5000 -162 163 1 0.352 7500 -165 166 1 0.330 5000 -166 167 1 0.380 5000 -170 171 1 0.330 7500 -173 174 1 0.287 7500 -175 176 1 0.330 5000 -176 177 1 0.380 5000 -178 179 1 0.352 5000 -180 181 1 0.363 7500 -182 183 1 0.341 7500 -184 185 1 0.352 5000 -188 189 1 0.330 7500 -190 191 1 0.341 7500 -192 193 1 0.287 7500 -196 197 1 0.363 7500 -198 199 1 0.363 7500 -200 201 1 0.287 7500 -202 203 1 0.287 7500 -204 205 1 0.352 7500 -212 213 1 0.287 7500 -216 217 1 0.352 5000 -218 219 1 0.341 7500 -222 223 1 0.330 5000 -223 224 1 0.360 5000 -225 226 1 0.330 5000 -226 227 1 0.360 5000 -232 233 1 0.287 7500 -234 235 1 0.352 7500 -237 238 1 0.352 5000 -240 241 1 0.40 2500 -242 243 1 0.352 5000 -246 247 1 0.315 5000 -256 257 1 0.315 5000 -262 263 1 0.330 5000 -263 264 1 0.380 5000 -265 266 1 0.352 5000 -267 268 1 0.330 5000 -268 269 1 0.380 5000 -270 271 1 0.341 7500 -272 273 1 0.330 5000 -273 274 1 0.360 5000 -278 279 1 0.352 7500 -282 283 1 0.400 5000 -286 287 1 0.315 5000 -294 295 1 0.330 5000 -295 296 1 0.380 5000 -298 299 1 0.341 7500 -300 301 1 0.330 5000 -301 302 1 0.380 5000 -303 304 1 0.363 7500 - -#ifdef FLEXIBLE -; Side chain bonds - 4 5 1 0.292 1000000 - 7 8 1 0.340 1000000 - 7 9 1 0.340 1000000 - 8 9 1 0.290 1000000 - 20 21 1 0.270 1000000 - 22 23 1 0.270 1000000 - 24 25 1 0.270 1000000 - 35 36 1 0.320 1000000 - 35 37 1 0.300 1000000 - 36 37 1 0.270 1000000 - 46 47 1 0.300 1000000 - 46 48 1 0.300 1000000 - 47 49 1 0.285 1000000 - 48 49 1 0.285 1000000 - 47 48 1 0.300 1000000 - 55 56 1 0.300 1000000 - 55 57 1 0.300 1000000 - 56 58 1 0.285 1000000 - 57 58 1 0.285 1000000 - 56 57 1 0.300 1000000 - 67 68 1 0.335 1000000 - 68 71 1 0.412 1000000 - 70 71 1 0.293 1000000 - 67 70 1 0.404 1000000 - 68 70 1 0.470 1000000 - 72 73 1 0.292 1000000 - 76 77 1 0.270 1000000 - 78 79 1 0.270 1000000 - 84 85 1 0.340 1000000 - 84 86 1 0.340 1000000 - 85 86 1 0.290 1000000 - 94 95 1 0.340 1000000 - 94 96 1 0.340 1000000 - 95 96 1 0.290 1000000 - 99 100 1 0.305 1000000 -103 104 1 0.270 1000000 -105 106 1 0.305 1000000 -114 115 1 0.305 1000000 -121 122 1 0.305 1000000 -126 127 1 0.300 1000000 -126 128 1 0.300 1000000 -127 129 1 0.285 1000000 -128 129 1 0.285 1000000 -127 128 1 0.300 1000000 -131 132 1 0.341 1000000 -137 138 1 0.341 1000000 -147 148 1 0.335 1000000 -148 151 1 0.412 1000000 -150 151 1 0.293 1000000 -147 150 1 0.404 1000000 -148 150 1 0.470 1000000 -153 154 1 0.335 1000000 -154 157 1 0.412 1000000 -156 157 1 0.293 1000000 -153 156 1 0.404 1000000 -154 156 1 0.470 1000000 -168 169 1 0.305 1000000 -186 187 1 0.341 1000000 -194 195 1 0.270 1000000 -206 207 1 0.341 1000000 -208 209 1 0.305 1000000 -210 211 1 0.270 1000000 -214 215 1 0.292 1000000 -220 221 1 0.270 1000000 -228 229 1 0.341 1000000 -230 231 1 0.292 1000000 -244 245 1 0.270 1000000 -247 248 1 0.335 1000000 -248 251 1 0.412 1000000 -250 251 1 0.293 1000000 -247 250 1 0.404 1000000 -248 250 1 0.470 1000000 -252 253 1 0.292 1000000 -254 255 1 0.270 1000000 -257 258 1 0.335 1000000 -258 261 1 0.412 1000000 -260 261 1 0.293 1000000 -257 260 1 0.404 1000000 -258 260 1 0.470 1000000 -276 277 1 0.305 1000000 -280 281 1 0.292 1000000 -284 285 1 0.270 1000000 -287 288 1 0.335 1000000 -288 291 1 0.412 1000000 -290 291 1 0.293 1000000 -287 290 1 0.404 1000000 -288 290 1 0.470 1000000 -292 293 1 0.341 1000000 -#endif - -[ constraints ] - 15 299 1 0.24 ; Disulfide bridge - 75 271 1 0.24 ; Disulfide bridge -159 191 1 0.24 ; Disulfide bridge -183 219 1 0.24 ; Disulfide bridge - -; Backbone bonds - 10 11 1 0.33 - 11 14 1 0.310 - 14 16 1 0.310 - 16 18 1 0.310 - 18 20 1 0.310 - 20 22 1 0.310 - 22 24 1 0.310 - 24 26 1 0.310 - 26 28 1 0.310 - 28 31 1 0.310 - 31 34 1 0.33 - 59 61 1 0.33 - 61 63 1 0.310 - 63 64 1 0.310 - 64 66 1 0.310 - 66 72 1 0.310 - 72 74 1 0.310 - 74 76 1 0.310 - 76 78 1 0.310 - 78 80 1 0.310 - 80 83 1 0.310 - 83 87 1 0.310 - 87 89 1 0.310 - 89 91 1 0.33 -188 190 1 0.33 -190 192 1 0.310 -192 194 1 0.310 -194 196 1 0.310 -196 198 1 0.310 -198 200 1 0.33 -206 208 1 0.33 -208 210 1 0.310 -210 212 1 0.310 -212 214 1 0.310 -214 216 1 0.310 -216 218 1 0.310 -218 220 1 0.310 -220 222 1 0.310 -222 225 1 0.310 -225 228 1 0.310 -228 230 1 0.310 -230 232 1 0.310 -232 234 1 0.33 -237 239 1 0.33 -239 240 1 0.310 -240 242 1 0.310 -242 244 1 0.310 -244 246 1 0.33 -246 252 1 0.33 -252 254 1 0.310 -254 256 1 0.310 -256 262 1 0.310 -262 265 1 0.310 -265 267 1 0.310 -267 270 1 0.33 -278 280 1 0.33 -280 282 1 0.310 -282 284 1 0.310 -284 286 1 0.310 -286 292 1 0.310 -292 294 1 0.33 - -#ifndef FLEXIBLE -; Side chain bonds - 4 5 1 0.292 - 7 8 1 0.340 - 7 9 1 0.340 - 8 9 1 0.290 - 20 21 1 0.270 - 22 23 1 0.270 - 24 25 1 0.270 - 35 36 1 0.320 - 35 37 1 0.300 - 36 37 1 0.270 - 46 47 1 0.300 - 46 48 1 0.300 - 47 49 1 0.285 - 48 49 1 0.285 - 47 48 1 0.300 - 55 56 1 0.300 - 55 57 1 0.300 - 56 58 1 0.285 - 57 58 1 0.285 - 56 57 1 0.300 - 67 68 1 0.335 - 68 71 1 0.412 - 70 71 1 0.293 - 67 70 1 0.404 - 68 70 1 0.470 - 72 73 1 0.292 - 76 77 1 0.270 - 78 79 1 0.270 - 84 85 1 0.340 - 84 86 1 0.340 - 85 86 1 0.290 - 94 95 1 0.340 - 94 96 1 0.340 - 95 96 1 0.290 - 99 100 1 0.305 -103 104 1 0.270 -105 106 1 0.305 -114 115 1 0.305 -121 122 1 0.305 -126 127 1 0.300 -126 128 1 0.300 -127 129 1 0.285 -128 129 1 0.285 -127 128 1 0.300 -131 132 1 0.341 -137 138 1 0.341 -147 148 1 0.335 -148 151 1 0.412 -150 151 1 0.293 -147 150 1 0.404 -148 150 1 0.470 -153 154 1 0.335 -154 157 1 0.412 -156 157 1 0.293 -153 156 1 0.404 -154 156 1 0.470 -168 169 1 0.305 -186 187 1 0.341 -194 195 1 0.270 -206 207 1 0.341 -208 209 1 0.305 -210 211 1 0.270 -214 215 1 0.292 -220 221 1 0.270 -228 229 1 0.341 -230 231 1 0.292 -244 245 1 0.270 -247 248 1 0.335 -248 251 1 0.412 -250 251 1 0.293 -247 250 1 0.404 -248 250 1 0.470 -252 253 1 0.292 -254 255 1 0.270 -257 258 1 0.335 -258 261 1 0.412 -260 261 1 0.293 -257 260 1 0.404 -258 260 1 0.470 -276 277 1 0.305 -280 281 1 0.292 -284 285 1 0.270 -287 288 1 0.335 -288 291 1 0.412 -290 291 1 0.293 -287 290 1 0.404 -288 290 1 0.470 -292 293 1 0.341 -#endif - -[ angles ] -; BBB angles - 6 10 11 10 127 20 - 10 11 14 10 127 20 - 11 14 16 2 96 700 - 14 16 18 2 96 700 - 16 18 20 2 96 700 - 18 20 22 2 96 700 - 20 22 24 2 96 700 - 22 24 26 2 96 700 - 24 26 28 2 96 700 - 26 28 31 2 96 700 - 28 31 34 10 100 20 - 31 34 38 10 100 20 - 54 59 61 10 127 20 - 59 61 63 10 127 20 - 61 63 64 2 96 700 - 63 64 66 2 96 700 - 64 66 72 2 96 700 - 66 72 74 2 96 700 - 72 74 76 2 96 700 - 74 76 78 2 96 700 - 76 78 80 2 96 700 - 78 80 83 2 96 700 - 80 83 87 2 96 700 - 83 87 89 2 96 700 - 87 89 91 10 100 20 - 89 91 93 10 100 20 -186 188 190 10 130 20 -188 190 192 10 134 25 -190 192 194 2 96 700 -192 194 196 2 96 700 -194 196 198 2 96 700 -196 198 200 10 130 20 -198 200 202 10 130 20 -204 206 208 10 127 20 -206 208 210 10 127 20 -208 210 212 2 96 700 -210 212 214 2 96 700 -212 214 216 2 96 700 -214 216 218 2 96 700 -216 218 220 2 96 700 -218 220 222 2 96 700 -220 222 225 2 96 700 -222 225 228 2 96 700 -225 228 230 2 96 700 -228 230 232 2 96 700 -230 232 234 10 100 20 -232 234 236 10 100 20 -236 237 239 10 130 20 -237 239 240 10 130 20 -239 240 242 2 96 700 -240 242 244 2 96 700 -242 244 246 10 130 20 -244 246 252 10 130 20 -246 252 254 10 130 20 -252 254 256 2 96 700 -254 256 262 2 96 700 -256 262 265 2 96 700 -262 265 267 2 96 700 -265 267 270 10 100 20 -267 270 272 10 100 20 -276 278 280 10 127 20 -278 280 282 10 127 20 -280 282 284 2 96 700 -282 284 286 2 96 700 -284 286 292 2 96 700 -286 292 294 10 100 20 -292 294 297 10 100 20 - 1 4 6 10 127 20 - 4 6 10 10 127 20 - 41 43 45 10 100 20 - 43 45 50 10 100 20 - 45 50 53 10 100 20 - 50 53 54 10 100 20 - 53 54 59 10 100 20 - 91 93 97 10 100 20 - 93 97 99 10 100 20 - 97 99 101 10 100 20 -101 103 105 10 100 20 -103 105 107 10 127 20 -105 107 109 10 134 25 -107 109 112 10 127 20 -109 112 114 10 100 20 -118 119 121 10 127 20 -119 121 123 10 127 20 -121 123 125 10 134 25 -123 125 130 10 100 20 -125 130 131 10 100 20 -133 135 137 10 100 20 -135 137 139 10 100 20 -137 139 141 10 100 20 -139 141 143 10 100 20 -152 158 160 10 100 20 -158 160 162 10 127 20 -160 162 164 10 127 20 -184 186 188 10 127 20 -165 168 170 10 127 20 -168 170 172 10 100 20 -170 172 173 10 100 20 -114 116 118 10 100 20 -116 118 119 10 100 20 -162 164 165 10 127 20 -164 165 168 10 127 20 -182 184 186 10 100 20 -200 202 204 10 130 20 -202 204 206 10 127 20 -234 236 237 10 100 20 -272 275 276 10 100 20 -275 276 278 10 100 20 - 34 38 39 10 100 20 - 38 39 41 10 100 20 - 39 41 43 10 100 20 - 99 101 103 10 100 20 -112 114 116 10 100 20 -146 152 158 10 100 20 -172 173 175 10 100 20 -173 175 178 10 127 20 -175 178 180 10 100 20 -178 180 182 10 100 20 -180 182 184 10 100 20 -294 297 298 10 100 20 -297 298 300 10 100 20 -298 300 303 10 127 20 -130 131 133 10 100 20 -131 133 135 10 100 20 -141 143 146 10 100 20 -143 146 152 10 100 20 -270 272 275 10 100 20 - -; BBS angles regular martini - 1 4 5 2 100 25 - 4 6 7 2 100 25 - 10 11 12 2 100 25 - 11 14 15 2 100 25 - 14 16 17 2 100 25 - 16 18 19 2 100 25 - 18 20 21 2 100 25 - 20 22 23 2 100 25 - 22 24 25 2 100 25 - 24 26 27 2 100 25 - 26 28 29 2 100 25 - 28 31 32 2 100 25 - 31 34 35 2 100 25 - 38 39 40 2 100 25 - 39 41 42 2 100 25 - 41 43 44 2 100 25 - 43 45 46 2 100 25 - 45 50 51 2 100 25 - 53 54 55 2 100 25 - 54 59 60 2 100 25 - 59 61 62 2 100 25 - 63 64 65 2 100 25 - 64 66 67 2 100 25 - 66 72 73 2 100 25 - 72 74 75 2 100 25 - 74 76 77 2 100 25 - 76 78 79 2 100 25 - 78 80 81 2 100 25 - 80 83 84 2 100 25 - 83 87 88 2 100 25 - 87 89 90 2 100 25 - 89 91 92 2 100 25 - 91 93 94 2 100 25 - 93 97 98 2 100 25 - 97 99 100 2 100 25 - 99 101 102 2 100 25 -101 103 104 2 100 25 -103 105 106 2 100 25 -105 107 108 2 100 25 -107 109 110 2 100 25 -109 112 113 2 100 25 -112 114 115 2 100 25 -114 116 117 2 100 25 -118 119 120 2 100 25 -119 121 122 2 100 25 -121 123 124 2 100 25 -123 125 126 2 100 25 -130 131 132 2 100 25 -131 133 134 2 100 25 -133 135 136 2 100 25 -135 137 138 2 100 25 -137 139 140 2 100 25 -139 141 142 2 100 25 -141 143 144 2 100 25 -143 146 147 2 100 25 -146 152 153 2 100 25 -152 158 159 2 100 25 -158 160 161 2 100 25 -160 162 163 2 100 25 -164 165 166 2 100 25 -165 168 169 2 100 25 -168 170 171 2 100 25 -172 173 174 2 100 25 -173 175 176 2 100 25 -175 178 179 2 100 25 -178 180 181 2 100 25 -180 182 183 2 100 25 -182 184 185 2 100 25 -184 186 187 2 100 25 -186 188 189 2 100 25 -188 190 191 2 100 25 -190 192 193 2 100 25 -192 194 195 2 100 25 -194 196 197 2 100 25 -196 198 199 2 100 25 -198 200 201 2 100 25 -200 202 203 2 100 25 -202 204 205 2 100 25 -204 206 207 2 100 25 -206 208 209 2 100 25 -208 210 211 2 100 25 -210 212 213 2 100 25 -212 214 215 2 100 25 -214 216 217 2 100 25 -216 218 219 2 100 25 -218 220 221 2 100 25 -220 222 223 2 100 25 -222 225 226 2 100 25 -225 228 229 2 100 25 -228 230 231 2 100 25 -230 232 233 2 100 25 -232 234 235 2 100 25 -236 237 238 2 100 25 -239 240 241 2 100 25 -240 242 243 2 100 25 -242 244 245 2 100 25 -244 246 247 2 100 25 -246 252 253 2 100 25 -252 254 255 2 100 25 -254 256 257 2 100 25 -256 262 263 2 100 25 -262 265 266 2 100 25 -265 267 268 2 100 25 -267 270 271 2 100 25 -270 272 273 2 100 25 -275 276 277 2 100 25 -276 278 279 2 100 25 -278 280 281 2 100 25 -280 282 283 2 100 25 -282 284 285 2 100 25 -284 286 287 2 100 25 -286 292 293 2 100 25 -292 294 295 2 100 25 -297 298 299 2 100 25 -298 300 301 2 100 25 -300 303 304 2 100 25 - -; First SBB regular martini - 2 1 4 2 100 25 - -; SC-BB-BB and BB-BB-SC scFix - 2 1 4 10 100 15 ; SC-BB-BB - 5 4 6 10 100 15 ; SC-BB-BB - 7 6 10 10 100 15 ; SC-BB-BB - 12 11 14 10 100 15 ; SC-BB-BB - 15 14 16 10 100 15 ; SC-BB-BB - 17 16 18 10 100 15 ; SC-BB-BB - 19 18 20 10 100 15 ; SC-BB-BB - 21 20 22 10 100 15 ; SC-BB-BB - 23 22 24 10 100 15 ; SC-BB-BB - 25 24 26 10 100 15 ; SC-BB-BB - 27 26 28 10 100 15 ; SC-BB-BB - 29 28 31 10 100 15 ; SC-BB-BB - 32 31 34 10 100 15 ; SC-BB-BB - 35 34 38 10 100 15 ; SC-BB-BB - 40 39 41 10 100 15 ; SC-BB-BB - 42 41 43 10 100 15 ; SC-BB-BB - 44 43 45 10 100 15 ; SC-BB-BB - 46 45 50 10 100 15 ; SC-BB-BB - 51 50 53 10 100 15 ; SC-BB-BB - 55 54 59 10 100 15 ; SC-BB-BB - 60 59 61 10 100 15 ; SC-BB-BB - 62 61 63 10 100 15 ; SC-BB-BB - 65 64 66 10 100 15 ; SC-BB-BB - 67 66 72 10 100 15 ; SC-BB-BB - 73 72 74 10 100 15 ; SC-BB-BB - 75 74 76 10 100 15 ; SC-BB-BB - 77 76 78 10 100 15 ; SC-BB-BB - 79 78 80 10 100 15 ; SC-BB-BB - 81 80 83 10 100 15 ; SC-BB-BB - 84 83 87 10 100 15 ; SC-BB-BB - 88 87 89 10 100 15 ; SC-BB-BB - 90 89 91 10 100 15 ; SC-BB-BB - 92 91 93 10 100 15 ; SC-BB-BB - 94 93 97 10 100 15 ; SC-BB-BB - 98 97 99 10 100 15 ; SC-BB-BB -100 99 101 10 100 15 ; SC-BB-BB -102 101 103 10 100 15 ; SC-BB-BB -104 103 105 10 100 15 ; SC-BB-BB -106 105 107 10 100 15 ; SC-BB-BB -108 107 109 10 100 15 ; SC-BB-BB -110 109 112 10 100 15 ; SC-BB-BB -113 112 114 10 100 15 ; SC-BB-BB -115 114 116 10 100 15 ; SC-BB-BB -117 116 118 10 100 15 ; SC-BB-BB -120 119 121 10 100 15 ; SC-BB-BB -122 121 123 10 100 15 ; SC-BB-BB -124 123 125 10 100 15 ; SC-BB-BB -126 125 130 10 100 15 ; SC-BB-BB -132 131 133 10 100 15 ; SC-BB-BB -134 133 135 10 100 15 ; SC-BB-BB -136 135 137 10 100 15 ; SC-BB-BB -138 137 139 10 100 15 ; SC-BB-BB -140 139 141 10 100 15 ; SC-BB-BB -142 141 143 10 100 15 ; SC-BB-BB -144 143 146 10 100 15 ; SC-BB-BB -147 146 152 10 100 15 ; SC-BB-BB -153 152 158 10 100 15 ; SC-BB-BB -159 158 160 10 100 15 ; SC-BB-BB -161 160 162 10 100 15 ; SC-BB-BB -163 162 164 10 100 15 ; SC-BB-BB -166 165 168 10 100 15 ; SC-BB-BB -169 168 170 10 100 15 ; SC-BB-BB -171 170 172 10 100 15 ; SC-BB-BB -174 173 175 10 100 15 ; SC-BB-BB -176 175 178 10 100 15 ; SC-BB-BB -179 178 180 10 100 15 ; SC-BB-BB -181 180 182 10 100 15 ; SC-BB-BB -183 182 184 10 100 15 ; SC-BB-BB -185 184 186 10 100 15 ; SC-BB-BB -187 186 188 10 100 15 ; SC-BB-BB -189 188 190 10 100 15 ; SC-BB-BB -191 190 192 10 100 15 ; SC-BB-BB -193 192 194 10 100 15 ; SC-BB-BB -195 194 196 10 100 15 ; SC-BB-BB -197 196 198 10 100 15 ; SC-BB-BB -199 198 200 10 100 15 ; SC-BB-BB -201 200 202 10 100 15 ; SC-BB-BB -203 202 204 10 100 15 ; SC-BB-BB -205 204 206 10 100 15 ; SC-BB-BB -207 206 208 10 100 15 ; SC-BB-BB -209 208 210 10 100 15 ; SC-BB-BB -211 210 212 10 100 15 ; SC-BB-BB -213 212 214 10 100 15 ; SC-BB-BB -215 214 216 10 100 15 ; SC-BB-BB -217 216 218 10 100 15 ; SC-BB-BB -219 218 220 10 100 15 ; SC-BB-BB -221 220 222 10 100 15 ; SC-BB-BB -223 222 225 10 100 15 ; SC-BB-BB -226 225 228 10 100 15 ; SC-BB-BB -229 228 230 10 100 15 ; SC-BB-BB -231 230 232 10 100 15 ; SC-BB-BB -233 232 234 10 100 15 ; SC-BB-BB -235 234 236 10 100 15 ; SC-BB-BB -238 237 239 10 100 15 ; SC-BB-BB -241 240 242 10 100 15 ; SC-BB-BB -243 242 244 10 100 15 ; SC-BB-BB -245 244 246 10 100 15 ; SC-BB-BB -247 246 252 10 100 15 ; SC-BB-BB -253 252 254 10 100 15 ; SC-BB-BB -255 254 256 10 100 15 ; SC-BB-BB -257 256 262 10 100 15 ; SC-BB-BB -263 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183 1 -159.3 75 1 ; SC-BB-BB-SC -183 182 184 185 1 18.3 75 1 ; SC-BB-BB-SC -185 184 186 187 1 -46.2 75 1 ; SC-BB-BB-SC -187 186 188 189 1 69.5 75 1 ; SC-BB-BB-SC -189 188 190 191 1 47.0 75 1 ; SC-BB-BB-SC -191 190 192 193 1 -114.4 75 1 ; SC-BB-BB-SC -193 192 194 195 1 -132.7 75 1 ; SC-BB-BB-SC -195 194 196 197 1 -157.0 75 1 ; SC-BB-BB-SC -197 196 198 199 1 -170.4 75 1 ; SC-BB-BB-SC -199 198 200 201 1 -87.6 75 1 ; SC-BB-BB-SC -201 200 202 203 1 85.2 75 1 ; SC-BB-BB-SC -203 202 204 205 1 138.2 75 1 ; SC-BB-BB-SC -205 204 206 207 1 66.9 75 1 ; SC-BB-BB-SC -207 206 208 209 1 -87.4 75 1 ; SC-BB-BB-SC -209 208 210 211 1 -138.0 75 1 ; SC-BB-BB-SC -211 210 212 213 1 -144.5 75 1 ; SC-BB-BB-SC -213 212 214 215 1 -145.4 75 1 ; SC-BB-BB-SC -215 214 216 217 1 -145.1 75 1 ; SC-BB-BB-SC -217 216 218 219 1 -162.0 75 1 ; SC-BB-BB-SC -219 218 220 221 1 -103.8 75 1 ; SC-BB-BB-SC -221 220 222 223 1 -141.5 75 1 ; SC-BB-BB-SC -223 222 225 226 1 -162.6 75 1 ; SC-BB-BB-SC -226 225 228 229 1 -127.6 75 1 ; 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303 304 1 -8.7 75 1 ; SC-BB-BB-SC - 6 10 11 12 1 -98.9 75 1 ; BB-BB-BB-SC - 7 6 10 11 1 -100.3 75 1 ; SC-BB-BB-BB - 34 38 39 40 1 138.6 75 1 ; BB-BB-BB-SC - 35 34 38 39 1 -144.1 75 1 ; SC-BB-BB-BB - 50 53 54 55 1 114.9 75 1 ; BB-BB-BB-SC - 51 50 53 54 1 -97.5 75 1 ; SC-BB-BB-BB - 61 63 64 65 1 92.4 75 1 ; BB-BB-BB-SC - 62 61 63 64 1 44.4 75 1 ; SC-BB-BB-BB -116 118 119 120 1 140.2 75 1 ; BB-BB-BB-SC -117 116 118 119 1 -157.4 75 1 ; SC-BB-BB-BB -125 130 131 132 1 44.0 75 1 ; BB-BB-BB-SC -126 125 130 131 1 -26.0 75 1 ; SC-BB-BB-BB -162 164 165 166 1 114.1 75 1 ; BB-BB-BB-SC -163 162 164 165 1 178.3 75 1 ; SC-BB-BB-BB -170 172 173 174 1 153.7 75 1 ; BB-BB-BB-SC -171 170 172 173 1 56.8 75 1 ; SC-BB-BB-BB -234 236 237 238 1 80.8 75 1 ; BB-BB-BB-SC -235 234 236 237 1 -115.7 75 1 ; SC-BB-BB-BB -237 239 240 241 1 25.4 75 1 ; BB-BB-BB-SC -238 237 239 240 1 104.0 75 1 ; SC-BB-BB-BB -272 275 276 277 1 134.9 75 1 ; BB-BB-BB-SC -273 272 275 276 1 31.9 75 1 ; SC-BB-BB-BB -294 297 298 299 1 130.9 75 1 ; BB-BB-BB-SC -295 294 297 298 1 37.9 75 1 ; SC-BB-BB-BB - -[ exclusions ] - 6 7 8 9 - 7 8 9 - 8 9 - 34 35 36 37 - 35 36 37 - 36 37 - 45 46 47 48 49 - 46 47 48 49 - 47 48 49 - 48 49 - 54 55 56 57 58 - 55 56 57 58 - 56 57 58 - 57 58 - 66 67 68 69 70 71 - 67 68 69 70 71 - 68 69 70 71 - 69 70 71 - 70 71 - 83 84 85 86 - 84 85 86 - 85 86 - 93 94 95 96 - 94 95 96 - 95 96 -125 126 127 128 129 -126 127 128 129 -127 128 129 -128 129 -146 147 148 149 150 151 -147 148 149 150 151 -148 149 150 151 -149 150 151 -150 151 -152 153 154 155 156 157 -153 154 155 156 157 -154 155 156 157 -155 156 157 -156 157 -246 247 248 249 250 251 -247 248 249 250 251 -248 249 250 251 -249 250 251 -250 251 -256 257 258 259 260 261 -257 258 259 260 261 -258 259 260 261 -259 260 261 -260 261 -286 287 288 289 290 291 -287 288 289 290 291 -288 289 290 291 -289 290 291 -290 291 - -; Go model exclusion - 16 6 - 18 6 - 18 10 - 20 11 - 22 14 - 24 16 - 26 18 - 28 20 - 31 22 - 34 24 - 38 26 - 39 26 - 41 28 - 45 38 - 54 43 - 59 41 - 59 43 - 61 20 - 61 26 - 61 28 - 61 41 - 64 53 - 64 54 - 66 26 - 66 39 - 66 54 - 66 59 - 72 11 - 72 20 - 72 26 - 72 61 - 74 63 - 76 64 - 78 18 - 78 66 - 80 72 - 83 74 - 87 76 - 89 78 - 91 78 - 91 80 - 93 1 - 93 4 - 93 6 - 93 11 - 93 18 - 93 72 - 93 78 - 93 80 - 97 1 - 97 4 - 99 1 - 99 6 -101 1 -103 89 -107 87 -118 109 -119 109 -119 112 -121 105 -121 107 -121 109 -121 112 -123 105 -123 107 -123 112 -125 103 -125 105 -130 89 -130 99 -130 103 -131 6 -131 18 -131 78 -131 87 -131 89 -131 93 -131 97 -131 99 -133 76 -133 78 -133 87 -135 87 -135 89 -135 103 -135 105 -135 107 -135 123 -135 125 -137 123 -137 125 -139 112 -139 119 -139 121 -139 123 -141 119 -141 121 -141 125 -143 116 -143 119 -152 137 -152 139 -158 125 -158 141 -162 121 -162 141 -165 121 -168 118 -168 119 -168 141 -168 143 -170 143 -173 141 -173 143 -173 158 -175 143 -175 146 -178 146 -178 152 -178 158 -178 160 -180 146 -180 152 -182 152 -186 152 -186 160 -186 178 -190 125 -190 141 -194 186 -196 125 -196 130 -196 137 -196 158 -196 186 -198 99 -198 101 -198 103 -198 105 -198 125 -198 130 -200 99 -200 192 -202 1 -202 6 -202 99 -206 18 -206 24 -206 26 -206 34 -206 99 -206 131 -208 31 -208 34 -210 186 -210 194 -210 196 -212 131 -212 137 -212 196 -214 34 -214 39 -214 206 -216 208 -218 137 -218 152 -218 196 -218 210 -220 66 -220 133 -220 137 -220 212 -222 34 -222 38 -222 39 -222 45 -222 214 -225 152 -225 182 -225 216 -228 137 -228 152 -228 218 -230 45 -230 50 -230 54 -230 220 -232 45 -232 50 -232 222 -234 225 -239 54 -239 230 -240 54 -240 64 -240 66 -240 76 -240 230 -244 228 -246 66 -246 87 -246 133 -246 135 -246 228 -246 230 -254 83 -254 87 -256 64 -256 76 -256 240 -256 242 -262 242 -262 244 -262 246 -265 252 -267 83 -267 254 -270 83 -270 254 -270 256 -272 242 -272 256 -272 262 -276 267 -280 59 -280 63 -280 64 -280 74 -280 270 -284 11 -286 11 -286 63 -286 72 -286 74 -286 80 -286 276 -292 11 -292 20 -292 61 -292 63 -292 72 -294 11 -294 282 -303 20 -303 22 -303 28 -303 292 - -[ dihedrals ] - 49 47 48 46 2 180.0 50.0 - 58 56 57 55 2 180.0 50.0 - 71 70 68 67 2 180.0 100.0 -129 127 128 126 2 180.0 50.0 -151 150 148 147 2 180.0 100.0 -157 156 154 153 2 180.0 100.0 -251 250 248 247 2 180.0 100.0 -261 260 258 257 2 180.0 100.0 -291 290 288 287 2 180.0 100.0 - -[ virtual_sitesn ] - 69 2 71 70 68 67 -149 2 151 150 148 147 -155 2 157 156 154 153 -249 2 251 250 248 247 -259 2 261 260 258 257 -289 2 291 290 288 287 - -; Virtual go site -305 1 1 -306 1 4 -307 1 6 -308 1 10 -309 1 11 -310 1 14 -311 1 16 -312 1 18 -313 1 20 -314 1 22 -315 1 24 -316 1 26 -317 1 28 -318 1 31 -319 1 34 -320 1 38 -321 1 39 -322 1 41 -323 1 43 -324 1 45 -325 1 50 -326 1 53 -327 1 54 -328 1 59 -329 1 61 -330 1 63 -331 1 64 -332 1 66 -333 1 72 -334 1 74 -335 1 76 -336 1 78 -337 1 80 -338 1 83 -339 1 87 -340 1 89 -341 1 91 -342 1 93 -343 1 97 -344 1 99 -345 1 101 -346 1 103 -347 1 105 -348 1 107 -349 1 109 -350 1 112 -351 1 114 -352 1 116 -353 1 118 -354 1 119 -355 1 121 -356 1 123 -357 1 125 -358 1 130 -359 1 131 -360 1 133 -361 1 135 -362 1 137 -363 1 139 -364 1 141 -365 1 143 -366 1 146 -367 1 152 -368 1 158 -369 1 160 -370 1 162 -371 1 164 -372 1 165 -373 1 168 -374 1 170 -375 1 172 -376 1 173 -377 1 175 -378 1 178 -379 1 180 -380 1 182 -381 1 184 -382 1 186 -383 1 188 -384 1 190 -385 1 192 -386 1 194 -387 1 196 -388 1 198 -389 1 200 -390 1 202 -391 1 204 -392 1 206 -393 1 208 -394 1 210 -395 1 212 -396 1 214 -397 1 216 -398 1 218 -399 1 220 -400 1 222 -401 1 225 -402 1 228 -403 1 230 -404 1 232 -405 1 234 -406 1 236 -407 1 237 -408 1 239 -409 1 240 -410 1 242 -411 1 244 -412 1 246 -413 1 252 -414 1 254 -415 1 256 -416 1 262 -417 1 265 -418 1 267 -419 1 270 -420 1 272 -421 1 275 -422 1 276 -423 1 278 -424 1 280 -425 1 282 -426 1 284 -427 1 286 -428 1 292 -429 1 294 -430 1 297 -431 1 298 -432 1 300 -433 1 303 - diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp new file mode 100644 index 000000000..bfc214c64 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp @@ -0,0 +1,1669 @@ +; This file was generated using the following command: +; /local/lborge01/martinize_stuff/dev_go/devmartinize/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go -go-map ../map.map -water-bias -water-bias-eps E:-.5 C:1.0 H:-1.0 +; martinize with vermouth 0.9.7.dev79 +; The following sequence of secondary structure +; was used for the full system: +; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC + +; Pleas cite the following papers: +; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 + +[ moleculetype ] +molecule_0 1 + +[ atoms ] + 1 Q5 1 LYS BB 1 1 + 2 SC3 1 LYS SC1 2 0.0 + 3 SQ4p 1 LYS SC2 3 1.0 + 4 SP2 2 VAL BB 4 0.0 + 5 SC3 2 VAL SC1 5 0.0 + 6 P2 3 PHE BB 6 0.0 + 7 SC4 3 PHE SC1 7 0.0 + 8 TC5 3 PHE SC2 8 0.0 + 9 TC5 3 PHE SC3 9 0.0 + 10 SP1 4 GLY BB 10 0.0 + 11 P2 5 ARG BB 11 0.0 + 12 SC3 5 ARG SC1 12 0.0 + 13 SQ3p 5 ARG SC2 13 1.0 + 14 P2 6 CYS BB 14 0.0 + 15 TC6 6 CYS SC1 15 0.0 + 16 P2 7 GLU BB 16 0.0 + 17 Q5n 7 GLU SC1 17 -1.0 + 18 P2 8 LEU BB 18 0.0 + 19 SC2 8 LEU SC1 19 0.0 + 20 SP2 9 ALA BB 20 0.0 + 21 TC3 9 ALA SC1 21 0.0 + 22 SP2 10 ALA BB 22 0.0 + 23 TC3 10 ALA SC1 23 0.0 + 24 SP2 11 ALA BB 24 0.0 + 25 TC3 11 ALA SC1 25 0.0 + 26 P2 12 MET BB 26 0.0 + 27 C6 12 MET SC1 27 0.0 + 28 P2 13 LYS BB 28 0.0 + 29 SC3 13 LYS SC1 29 0.0 + 30 SQ4p 13 LYS SC2 30 1.0 + 31 P2 14 ARG BB 31 0.0 + 32 SC3 14 ARG SC1 32 0.0 + 33 SQ3p 14 ARG SC2 33 1.0 + 34 P2 15 HIS BB 34 0.0 + 35 TC4 15 HIS SC1 35 0.0 + 36 TN6d 15 HIS SC2 36 0.0 + 37 TN5a 15 HIS SC3 37 0.0 + 38 SP1 16 GLY BB 38 0.0 + 39 P2 17 LEU BB 39 0.0 + 40 SC2 17 LEU SC1 40 0.0 + 41 P2 18 ASP BB 41 0.0 + 42 SQ5n 18 ASP SC1 42 -1.0 + 43 P2 19 ASN BB 43 0.0 + 44 SP5 19 ASN SC1 44 0.0 + 45 P2 20 TYR BB 45 0.0 + 46 TC4 20 TYR SC1 46 0.0 + 47 TC5 20 TYR SC2 47 0.0 + 48 TC5 20 TYR SC3 48 0.0 + 49 TN6 20 TYR SC4 49 0.0 + 50 P2 21 ARG BB 50 0.0 + 51 SC3 21 ARG SC1 51 0.0 + 52 SQ3p 21 ARG SC2 52 1.0 + 53 SP1 22 GLY BB 53 0.0 + 54 P2 23 TYR BB 54 0.0 + 55 TC4 23 TYR SC1 55 0.0 + 56 TC5 23 TYR SC2 56 0.0 + 57 TC5 23 TYR SC3 57 0.0 + 58 TN6 23 TYR SC4 58 0.0 + 59 P2 24 SER BB 59 0.0 + 60 TP1 24 SER SC1 60 0.0 + 61 P2 25 LEU BB 61 0.0 + 62 SC2 25 LEU SC1 62 0.0 + 63 SP1 26 GLY BB 63 0.0 + 64 P2 27 ASN BB 64 0.0 + 65 SP5 27 ASN SC1 65 0.0 + 66 P2 28 TRP BB 66 0.0 + 67 TC4 28 TRP SC1 67 0.0 36.0 + 68 TN6d 28 TRP SC2 68 0.0 36.0 + 69 TC5 28 TRP SC3 69 0.0 0.0 + 70 TC5 28 TRP SC4 70 0.0 36.0 + 71 TC5 28 TRP SC5 71 0.0 36.0 + 72 SP2 29 VAL BB 72 0.0 + 73 SC3 29 VAL SC1 73 0.0 + 74 P2 30 CYS BB 74 0.0 + 75 TC6 30 CYS SC1 75 0.0 + 76 SP2 31 ALA BB 76 0.0 + 77 TC3 31 ALA SC1 77 0.0 + 78 SP2 32 ALA BB 78 0.0 + 79 TC3 32 ALA SC1 79 0.0 + 80 P2 33 LYS BB 80 0.0 + 81 SC3 33 LYS SC1 81 0.0 + 82 SQ4p 33 LYS SC2 82 1.0 + 83 P2 34 PHE BB 83 0.0 + 84 SC4 34 PHE SC1 84 0.0 + 85 TC5 34 PHE SC2 85 0.0 + 86 TC5 34 PHE SC3 86 0.0 + 87 P2 35 GLU BB 87 0.0 + 88 Q5n 35 GLU SC1 88 -1.0 + 89 P2 36 SER BB 89 0.0 + 90 TP1 36 SER SC1 90 0.0 + 91 P2 37 ASN BB 91 0.0 + 92 SP5 37 ASN SC1 92 0.0 + 93 P2 38 PHE BB 93 0.0 + 94 SC4 38 PHE SC1 94 0.0 + 95 TC5 38 PHE SC2 95 0.0 + 96 TC5 38 PHE SC3 96 0.0 + 97 P2 39 ASN BB 97 0.0 + 98 SP5 39 ASN SC1 98 0.0 + 99 P2 40 THR BB 99 0.0 +100 SP1 40 THR SC1 100 0.0 +101 P2 41 GLN BB 101 0.0 +102 P5 41 GLN SC1 102 0.0 +103 SP2 42 ALA BB 103 0.0 +104 TC3 42 ALA SC1 104 0.0 +105 P2 43 THR BB 105 0.0 +106 SP1 43 THR SC1 106 0.0 +107 P2 44 ASN BB 107 0.0 +108 SP5 44 ASN SC1 108 0.0 +109 P2 45 ARG BB 109 0.0 +110 SC3 45 ARG SC1 110 0.0 +111 SQ3p 45 ARG SC2 111 1.0 +112 P2 46 ASN BB 112 0.0 +113 SP5 46 ASN SC1 113 0.0 +114 P2 47 THR BB 114 0.0 +115 SP1 47 THR SC1 115 0.0 +116 P2 48 ASP BB 116 0.0 +117 SQ5n 48 ASP SC1 117 -1.0 +118 SP1 49 GLY BB 118 0.0 +119 P2 50 SER BB 119 0.0 +120 TP1 50 SER SC1 120 0.0 +121 P2 51 THR BB 121 0.0 +122 SP1 51 THR SC1 122 0.0 +123 P2 52 ASP BB 123 0.0 +124 SQ5n 52 ASP SC1 124 -1.0 +125 P2 53 TYR BB 125 0.0 +126 TC4 53 TYR SC1 126 0.0 +127 TC5 53 TYR SC2 127 0.0 +128 TC5 53 TYR SC3 128 0.0 +129 TN6 53 TYR SC4 129 0.0 +130 SP1 54 GLY BB 130 0.0 +131 P2 55 ILE BB 131 0.0 +132 SC2 55 ILE SC1 132 0.0 +133 P2 56 LEU BB 133 0.0 +134 SC2 56 LEU SC1 134 0.0 +135 P2 57 GLN BB 135 0.0 +136 P5 57 GLN SC1 136 0.0 +137 P2 58 ILE BB 137 0.0 +138 SC2 58 ILE SC1 138 0.0 +139 P2 59 ASN BB 139 0.0 +140 SP5 59 ASN SC1 140 0.0 +141 P2 60 SER BB 141 0.0 +142 TP1 60 SER SC1 142 0.0 +143 P2 61 ARG BB 143 0.0 +144 SC3 61 ARG SC1 144 0.0 +145 SQ3p 61 ARG SC2 145 1.0 +146 P2 62 TRP BB 146 0.0 +147 TC4 62 TRP SC1 147 0.0 36.0 +148 TN6d 62 TRP SC2 148 0.0 36.0 +149 TC5 62 TRP SC3 149 0.0 0.0 +150 TC5 62 TRP SC4 150 0.0 36.0 +151 TC5 62 TRP SC5 151 0.0 36.0 +152 P2 63 TRP BB 152 0.0 +153 TC4 63 TRP SC1 153 0.0 36.0 +154 TN6d 63 TRP SC2 154 0.0 36.0 +155 TC5 63 TRP SC3 155 0.0 0.0 +156 TC5 63 TRP SC4 156 0.0 36.0 +157 TC5 63 TRP SC5 157 0.0 36.0 +158 P2 64 CYS BB 158 0.0 +159 TC6 64 CYS SC1 159 0.0 +160 P2 65 ASN BB 160 0.0 +161 SP5 65 ASN SC1 161 0.0 +162 P2 66 ASP BB 162 0.0 +163 SQ5n 66 ASP SC1 163 -1.0 +164 SP1 67 GLY BB 164 0.0 +165 P2 68 ARG BB 165 0.0 +166 SC3 68 ARG SC1 166 0.0 +167 SQ3p 68 ARG SC2 167 1.0 +168 P2 69 THR BB 168 0.0 +169 SP1 69 THR SC1 169 0.0 +170 SP2a 70 PRO BB 170 0.0 +171 SC3 70 PRO SC1 171 0.0 +172 SP1 71 GLY BB 172 0.0 +173 P2 72 SER BB 173 0.0 +174 TP1 72 SER SC1 174 0.0 +175 P2 73 ARG BB 175 0.0 +176 SC3 73 ARG SC1 176 0.0 +177 SQ3p 73 ARG SC2 177 1.0 +178 P2 74 ASN BB 178 0.0 +179 SP5 74 ASN SC1 179 0.0 +180 P2 75 LEU BB 180 0.0 +181 SC2 75 LEU SC1 181 0.0 +182 P2 76 CYS BB 182 0.0 +183 TC6 76 CYS SC1 183 0.0 +184 P2 77 ASN BB 184 0.0 +185 SP5 77 ASN SC1 185 0.0 +186 P2 78 ILE BB 186 0.0 +187 SC2 78 ILE SC1 187 0.0 +188 SP2a 79 PRO BB 188 0.0 +189 SC3 79 PRO SC1 189 0.0 +190 P2 80 CYS BB 190 0.0 +191 TC6 80 CYS SC1 191 0.0 +192 P2 81 SER BB 192 0.0 +193 TP1 81 SER SC1 193 0.0 +194 SP2 82 ALA BB 194 0.0 +195 TC3 82 ALA SC1 195 0.0 +196 P2 83 LEU BB 196 0.0 +197 SC2 83 LEU SC1 197 0.0 +198 P2 84 LEU BB 198 0.0 +199 SC2 84 LEU SC1 199 0.0 +200 P2 85 SER BB 200 0.0 +201 TP1 85 SER SC1 201 0.0 +202 P2 86 SER BB 202 0.0 +203 TP1 86 SER SC1 203 0.0 +204 P2 87 ASP BB 204 0.0 +205 SQ5n 87 ASP SC1 205 -1.0 +206 P2 88 ILE BB 206 0.0 +207 SC2 88 ILE SC1 207 0.0 +208 P2 89 THR BB 208 0.0 +209 SP1 89 THR SC1 209 0.0 +210 SP2 90 ALA BB 210 0.0 +211 TC3 90 ALA SC1 211 0.0 +212 P2 91 SER BB 212 0.0 +213 TP1 91 SER SC1 213 0.0 +214 SP2 92 VAL BB 214 0.0 +215 SC3 92 VAL SC1 215 0.0 +216 P2 93 ASN BB 216 0.0 +217 SP5 93 ASN SC1 217 0.0 +218 P2 94 CYS BB 218 0.0 +219 TC6 94 CYS SC1 219 0.0 +220 SP2 95 ALA BB 220 0.0 +221 TC3 95 ALA SC1 221 0.0 +222 P2 96 LYS BB 222 0.0 +223 SC3 96 LYS SC1 223 0.0 +224 SQ4p 96 LYS SC2 224 1.0 +225 P2 97 LYS BB 225 0.0 +226 SC3 97 LYS SC1 226 0.0 +227 SQ4p 97 LYS SC2 227 1.0 +228 P2 98 ILE BB 228 0.0 +229 SC2 98 ILE SC1 229 0.0 +230 SP2 99 VAL BB 230 0.0 +231 SC3 99 VAL SC1 231 0.0 +232 P2 100 SER BB 232 0.0 +233 TP1 100 SER SC1 233 0.0 +234 P2 101 ASP BB 234 0.0 +235 SQ5n 101 ASP SC1 235 -1.0 +236 SP1 102 GLY BB 236 0.0 +237 P2 103 ASN BB 237 0.0 +238 SP5 103 ASN SC1 238 0.0 +239 SP1 104 GLY BB 239 0.0 +240 P2 105 MET BB 240 0.0 +241 C6 105 MET SC1 241 0.0 +242 P2 106 ASN BB 242 0.0 +243 SP5 106 ASN SC1 243 0.0 +244 SP2 107 ALA BB 244 0.0 +245 TC3 107 ALA SC1 245 0.0 +246 P2 108 TRP BB 246 0.0 +247 TC4 108 TRP SC1 247 0.0 36.0 +248 TN6d 108 TRP SC2 248 0.0 36.0 +249 TC5 108 TRP SC3 249 0.0 0.0 +250 TC5 108 TRP SC4 250 0.0 36.0 +251 TC5 108 TRP SC5 251 0.0 36.0 +252 SP2 109 VAL BB 252 0.0 +253 SC3 109 VAL SC1 253 0.0 +254 SP2 110 ALA BB 254 0.0 +255 TC3 110 ALA SC1 255 0.0 +256 P2 111 TRP BB 256 0.0 +257 TC4 111 TRP SC1 257 0.0 36.0 +258 TN6d 111 TRP SC2 258 0.0 36.0 +259 TC5 111 TRP SC3 259 0.0 0.0 +260 TC5 111 TRP SC4 260 0.0 36.0 +261 TC5 111 TRP SC5 261 0.0 36.0 +262 P2 112 ARG BB 262 0.0 +263 SC3 112 ARG SC1 263 0.0 +264 SQ3p 112 ARG SC2 264 1.0 +265 P2 113 ASN BB 265 0.0 +266 SP5 113 ASN SC1 266 0.0 +267 P2 114 ARG BB 267 0.0 +268 SC3 114 ARG SC1 268 0.0 +269 SQ3p 114 ARG SC2 269 1.0 +270 P2 115 CYS BB 270 0.0 +271 TC6 115 CYS SC1 271 0.0 +272 P2 116 LYS BB 272 0.0 +273 SC3 116 LYS SC1 273 0.0 +274 SQ4p 116 LYS SC2 274 1.0 +275 SP1 117 GLY BB 275 0.0 +276 P2 118 THR BB 276 0.0 +277 SP1 118 THR SC1 277 0.0 +278 P2 119 ASP BB 278 0.0 +279 SQ5n 119 ASP SC1 279 -1.0 +280 SP2 120 VAL BB 280 0.0 +281 SC3 120 VAL SC1 281 0.0 +282 P2 121 GLN BB 282 0.0 +283 P5 121 GLN SC1 283 0.0 +284 SP2 122 ALA BB 284 0.0 +285 TC3 122 ALA SC1 285 0.0 +286 P2 123 TRP BB 286 0.0 +287 TC4 123 TRP SC1 287 0.0 36.0 +288 TN6d 123 TRP SC2 288 0.0 36.0 +289 TC5 123 TRP SC3 289 0.0 0.0 +290 TC5 123 TRP SC4 290 0.0 36.0 +291 TC5 123 TRP SC5 291 0.0 36.0 +292 P2 124 ILE BB 292 0.0 +293 SC2 124 ILE SC1 293 0.0 +294 P2 125 ARG BB 294 0.0 +295 SC3 125 ARG SC1 295 0.0 +296 SQ3p 125 ARG SC2 296 1.0 +297 SP1 126 GLY BB 297 0.0 +298 P2 127 CYS BB 298 0.0 +299 TC6 127 CYS SC1 299 0.0 +300 P2 128 ARG BB 300 0.0 +301 SC3 128 ARG SC1 301 0.0 +302 SQ3p 128 ARG SC2 302 1.0 +303 Q5 129 LEU BB 303 -1 +304 SC2 129 LEU SC1 304 0.0 +305 molecule_0_1 1 LYS CA 305 0 0.0 +306 molecule_0_2 2 VAL CA 306 0 0.0 +307 molecule_0_3 3 PHE CA 307 0 0.0 +308 molecule_0_4 4 GLY CA 308 0 0.0 +309 molecule_0_5 5 ARG CA 309 0 0.0 +310 molecule_0_6 6 CYS CA 310 0 0.0 +311 molecule_0_7 7 GLU CA 311 0 0.0 +312 molecule_0_8 8 LEU CA 312 0 0.0 +313 molecule_0_9 9 ALA CA 313 0 0.0 +314 molecule_0_10 10 ALA CA 314 0 0.0 +315 molecule_0_11 11 ALA CA 315 0 0.0 +316 molecule_0_12 12 MET CA 316 0 0.0 +317 molecule_0_13 13 LYS CA 317 0 0.0 +318 molecule_0_14 14 ARG CA 318 0 0.0 +319 molecule_0_15 15 HIS CA 319 0 0.0 +320 molecule_0_16 16 GLY CA 320 0 0.0 +321 molecule_0_17 17 LEU CA 321 0 0.0 +322 molecule_0_18 18 ASP CA 322 0 0.0 +323 molecule_0_19 19 ASN CA 323 0 0.0 +324 molecule_0_20 20 TYR CA 324 0 0.0 +325 molecule_0_21 21 ARG CA 325 0 0.0 +326 molecule_0_22 22 GLY CA 326 0 0.0 +327 molecule_0_23 23 TYR CA 327 0 0.0 +328 molecule_0_24 24 SER CA 328 0 0.0 +329 molecule_0_25 25 LEU CA 329 0 0.0 +330 molecule_0_26 26 GLY CA 330 0 0.0 +331 molecule_0_27 27 ASN CA 331 0 0.0 +332 molecule_0_28 28 TRP CA 332 0 0.0 +333 molecule_0_29 29 VAL CA 333 0 0.0 +334 molecule_0_30 30 CYS CA 334 0 0.0 +335 molecule_0_31 31 ALA CA 335 0 0.0 +336 molecule_0_32 32 ALA CA 336 0 0.0 +337 molecule_0_33 33 LYS CA 337 0 0.0 +338 molecule_0_34 34 PHE CA 338 0 0.0 +339 molecule_0_35 35 GLU CA 339 0 0.0 +340 molecule_0_36 36 SER CA 340 0 0.0 +341 molecule_0_37 37 ASN CA 341 0 0.0 +342 molecule_0_38 38 PHE CA 342 0 0.0 +343 molecule_0_39 39 ASN CA 343 0 0.0 +344 molecule_0_40 40 THR CA 344 0 0.0 +345 molecule_0_41 41 GLN CA 345 0 0.0 +346 molecule_0_42 42 ALA CA 346 0 0.0 +347 molecule_0_43 43 THR CA 347 0 0.0 +348 molecule_0_44 44 ASN CA 348 0 0.0 +349 molecule_0_45 45 ARG CA 349 0 0.0 +350 molecule_0_46 46 ASN CA 350 0 0.0 +351 molecule_0_47 47 THR CA 351 0 0.0 +352 molecule_0_48 48 ASP CA 352 0 0.0 +353 molecule_0_49 49 GLY CA 353 0 0.0 +354 molecule_0_50 50 SER CA 354 0 0.0 +355 molecule_0_51 51 THR CA 355 0 0.0 +356 molecule_0_52 52 ASP CA 356 0 0.0 +357 molecule_0_53 53 TYR CA 357 0 0.0 +358 molecule_0_54 54 GLY CA 358 0 0.0 +359 molecule_0_55 55 ILE CA 359 0 0.0 +360 molecule_0_56 56 LEU CA 360 0 0.0 +361 molecule_0_57 57 GLN CA 361 0 0.0 +362 molecule_0_58 58 ILE CA 362 0 0.0 +363 molecule_0_59 59 ASN CA 363 0 0.0 +364 molecule_0_60 60 SER CA 364 0 0.0 +365 molecule_0_61 61 ARG CA 365 0 0.0 +366 molecule_0_62 62 TRP CA 366 0 0.0 +367 molecule_0_63 63 TRP CA 367 0 0.0 +368 molecule_0_64 64 CYS CA 368 0 0.0 +369 molecule_0_65 65 ASN CA 369 0 0.0 +370 molecule_0_66 66 ASP CA 370 0 0.0 +371 molecule_0_67 67 GLY CA 371 0 0.0 +372 molecule_0_68 68 ARG CA 372 0 0.0 +373 molecule_0_69 69 THR CA 373 0 0.0 +374 molecule_0_70 70 PRO CA 374 0 0.0 +375 molecule_0_71 71 GLY CA 375 0 0.0 +376 molecule_0_72 72 SER CA 376 0 0.0 +377 molecule_0_73 73 ARG CA 377 0 0.0 +378 molecule_0_74 74 ASN CA 378 0 0.0 +379 molecule_0_75 75 LEU CA 379 0 0.0 +380 molecule_0_76 76 CYS CA 380 0 0.0 +381 molecule_0_77 77 ASN CA 381 0 0.0 +382 molecule_0_78 78 ILE CA 382 0 0.0 +383 molecule_0_79 79 PRO CA 383 0 0.0 +384 molecule_0_80 80 CYS CA 384 0 0.0 +385 molecule_0_81 81 SER CA 385 0 0.0 +386 molecule_0_82 82 ALA CA 386 0 0.0 +387 molecule_0_83 83 LEU CA 387 0 0.0 +388 molecule_0_84 84 LEU CA 388 0 0.0 +389 molecule_0_85 85 SER CA 389 0 0.0 +390 molecule_0_86 86 SER CA 390 0 0.0 +391 molecule_0_87 87 ASP CA 391 0 0.0 +392 molecule_0_88 88 ILE CA 392 0 0.0 +393 molecule_0_89 89 THR CA 393 0 0.0 +394 molecule_0_90 90 ALA CA 394 0 0.0 +395 molecule_0_91 91 SER CA 395 0 0.0 +396 molecule_0_92 92 VAL CA 396 0 0.0 +397 molecule_0_93 93 ASN CA 397 0 0.0 +398 molecule_0_94 94 CYS CA 398 0 0.0 +399 molecule_0_95 95 ALA CA 399 0 0.0 +400 molecule_0_96 96 LYS CA 400 0 0.0 +401 molecule_0_97 97 LYS CA 401 0 0.0 +402 molecule_0_98 98 ILE CA 402 0 0.0 +403 molecule_0_99 99 VAL CA 403 0 0.0 +404 molecule_0_100 100 SER CA 404 0 0.0 +405 molecule_0_101 101 ASP CA 405 0 0.0 +406 molecule_0_102 102 GLY CA 406 0 0.0 +407 molecule_0_103 103 ASN CA 407 0 0.0 +408 molecule_0_104 104 GLY CA 408 0 0.0 +409 molecule_0_105 105 MET CA 409 0 0.0 +410 molecule_0_106 106 ASN CA 410 0 0.0 +411 molecule_0_107 107 ALA CA 411 0 0.0 +412 molecule_0_108 108 TRP CA 412 0 0.0 +413 molecule_0_109 109 VAL CA 413 0 0.0 +414 molecule_0_110 110 ALA CA 414 0 0.0 +415 molecule_0_111 111 TRP CA 415 0 0.0 +416 molecule_0_112 112 ARG CA 416 0 0.0 +417 molecule_0_113 113 ASN CA 417 0 0.0 +418 molecule_0_114 114 ARG CA 418 0 0.0 +419 molecule_0_115 115 CYS CA 419 0 0.0 +420 molecule_0_116 116 LYS CA 420 0 0.0 +421 molecule_0_117 117 GLY CA 421 0 0.0 +422 molecule_0_118 118 THR CA 422 0 0.0 +423 molecule_0_119 119 ASP CA 423 0 0.0 +424 molecule_0_120 120 VAL CA 424 0 0.0 +425 molecule_0_121 121 GLN CA 425 0 0.0 +426 molecule_0_122 122 ALA CA 426 0 0.0 +427 molecule_0_123 123 TRP CA 427 0 0.0 +428 molecule_0_124 124 ILE CA 428 0 0.0 +429 molecule_0_125 125 ARG CA 429 0 0.0 +430 molecule_0_126 126 GLY CA 430 0 0.0 +431 molecule_0_127 127 CYS CA 431 0 0.0 +432 molecule_0_128 128 ARG CA 432 0 0.0 +433 molecule_0_129 129 LEU CA 433 0 0.0 + +[ bonds ] +; Backbone bonds + 1 4 1 0.350 4000 + 4 6 1 0.350 4000 + 6 10 1 0.350 4000 + 34 38 1 0.350 4000 + 38 39 1 0.350 4000 + 39 41 1 0.350 4000 + 41 43 1 0.350 4000 + 43 45 1 0.350 4000 + 45 50 1 0.350 4000 + 50 53 1 0.350 4000 + 53 54 1 0.350 4000 + 54 59 1 0.350 4000 + 91 93 1 0.350 4000 + 93 97 1 0.350 4000 + 97 99 1 0.350 4000 + 99 101 1 0.350 4000 +101 103 1 0.350 4000 +103 105 1 0.350 4000 +105 107 1 0.350 4000 +107 109 1 0.350 4000 +109 112 1 0.350 4000 +112 114 1 0.350 4000 +114 116 1 0.350 4000 +116 118 1 0.350 4000 +118 119 1 0.350 4000 +119 121 1 0.350 4000 +121 123 1 0.350 4000 +123 125 1 0.350 4000 +125 130 1 0.350 4000 +130 131 1 0.350 4000 +131 133 1 0.350 4000 +133 135 1 0.350 4000 +135 137 1 0.350 4000 +137 139 1 0.350 4000 +139 141 1 0.350 4000 +141 143 1 0.350 4000 +143 146 1 0.350 4000 +146 152 1 0.350 4000 +152 158 1 0.350 4000 +158 160 1 0.350 4000 +160 162 1 0.350 4000 +162 164 1 0.350 4000 +164 165 1 0.350 4000 +165 168 1 0.350 4000 +168 170 1 0.350 4000 +170 172 1 0.350 4000 +172 173 1 0.350 4000 +173 175 1 0.350 4000 +175 178 1 0.350 4000 +178 180 1 0.350 4000 +180 182 1 0.350 4000 +182 184 1 0.350 4000 +184 186 1 0.350 4000 +186 188 1 0.350 4000 +200 202 1 0.350 4000 +202 204 1 0.350 4000 +204 206 1 0.350 4000 +234 236 1 0.350 4000 +236 237 1 0.350 4000 +270 272 1 0.350 4000 +272 275 1 0.350 4000 +275 276 1 0.350 4000 +276 278 1 0.350 4000 +294 297 1 0.350 4000 +297 298 1 0.350 4000 +298 300 1 0.350 4000 +300 303 1 0.350 4000 + +; Side chain bonds + 1 2 1 0.330 5000 + 2 3 1 0.360 5000 + 6 7 1 0.325 7500 + 11 12 1 0.330 5000 + 12 13 1 0.380 5000 + 14 15 1 0.341 7500 + 16 17 1 0.400 5000 + 18 19 1 0.363 7500 + 26 27 1 0.40 2500 + 28 29 1 0.330 5000 + 29 30 1 0.360 5000 + 31 32 1 0.330 5000 + 32 33 1 0.380 5000 + 34 35 1 0.336 7500 + 39 40 1 0.363 7500 + 41 42 1 0.352 7500 + 43 44 1 0.352 5000 + 45 46 1 0.325 5000 + 50 51 1 0.330 5000 + 51 52 1 0.380 5000 + 54 55 1 0.325 5000 + 59 60 1 0.287 7500 + 61 62 1 0.363 7500 + 64 65 1 0.352 5000 + 66 67 1 0.315 5000 + 74 75 1 0.341 7500 + 80 81 1 0.330 5000 + 81 82 1 0.360 5000 + 83 84 1 0.325 7500 + 87 88 1 0.400 5000 + 89 90 1 0.287 7500 + 91 92 1 0.352 5000 + 93 94 1 0.325 7500 + 97 98 1 0.352 5000 +101 102 1 0.400 5000 +107 108 1 0.352 5000 +109 110 1 0.330 5000 +110 111 1 0.380 5000 +112 113 1 0.352 5000 +116 117 1 0.352 7500 +119 120 1 0.287 7500 +123 124 1 0.352 7500 +125 126 1 0.325 5000 +133 134 1 0.363 7500 +135 136 1 0.400 5000 +139 140 1 0.352 5000 +141 142 1 0.287 7500 +143 144 1 0.330 5000 +144 145 1 0.380 5000 +146 147 1 0.315 5000 +152 153 1 0.315 5000 +158 159 1 0.341 7500 +160 161 1 0.352 5000 +162 163 1 0.352 7500 +165 166 1 0.330 5000 +166 167 1 0.380 5000 +170 171 1 0.330 7500 +173 174 1 0.287 7500 +175 176 1 0.330 5000 +176 177 1 0.380 5000 +178 179 1 0.352 5000 +180 181 1 0.363 7500 +182 183 1 0.341 7500 +184 185 1 0.352 5000 +188 189 1 0.330 7500 +190 191 1 0.341 7500 +192 193 1 0.287 7500 +196 197 1 0.363 7500 +198 199 1 0.363 7500 +200 201 1 0.287 7500 +202 203 1 0.287 7500 +204 205 1 0.352 7500 +212 213 1 0.287 7500 +216 217 1 0.352 5000 +218 219 1 0.341 7500 +222 223 1 0.330 5000 +223 224 1 0.360 5000 +225 226 1 0.330 5000 +226 227 1 0.360 5000 +232 233 1 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b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top @@ -3,10 +3,10 @@ #include "go_atomtypes.itp" #include "go_nbparams.itp" -#include "molecule.itp" +#include "molecule_0.itp" [ system ] Title of the system [ molecules ] -molecule 1 +molecule_0 1