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76
doc/source/tutorials/6_adding_residues_links/files/ala-sep-ala.pdb
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ATOM 1 N ALA 2 5.892 6.590 0.772 1.00 0.00 N1+ | ||
ATOM 2 CA ALA 2 6.787 5.479 0.424 1.00 0.00 C | ||
ATOM 3 C ALA 2 7.358 5.632 -0.971 1.00 0.00 C | ||
ATOM 4 O ALA 2 6.678 6.097 -1.907 1.00 0.00 O | ||
ATOM 5 CB ALA 2 6.008 4.158 0.573 1.00 0.00 C | ||
ATOM 6 HA ALA 2 7.626 5.500 1.145 1.00 0.00 H | ||
ATOM 7 1HB ALA 2 5.609 4.032 1.598 1.00 0.00 H | ||
ATOM 8 2HB ALA 2 5.143 4.107 -0.117 1.00 0.00 H | ||
ATOM 9 3HB ALA 2 6.644 3.281 0.368 1.00 0.00 H | ||
ATOM 10 H01 ALA 2 5.554 6.479 1.717 1.00 0.00 H | ||
ATOM 11 H02 ALA 2 6.398 7.464 0.706 1.00 0.00 H | ||
ATOM 12 H03 ALA 2 5.108 6.609 0.131 1.00 0.00 H | ||
ATOM 13 N SER 3 8.566 5.235 -1.183 1.00 0.00 N | ||
ATOM 14 CA SER 3 9.087 4.998 -2.535 1.00 0.00 C | ||
ATOM 15 C SER 3 10.146 3.913 -2.485 1.00 0.00 C | ||
ATOM 16 O SER 3 11.339 4.171 -2.285 1.00 0.00 O | ||
ATOM 17 CB SER 3 9.611 6.290 -3.232 1.00 0.00 C | ||
ATOM 18 OG SER 3 10.708 6.960 -2.686 1.00 0.00 O | ||
ATOM 19 P SER 3 10.949 7.716 -1.502 1.00 0.00 P | ||
ATOM 20 O1 SER 3 11.988 7.174 -0.832 1.00 0.00 O | ||
ATOM 21 O2 SER 3 9.680 8.015 -0.948 1.00 0.00 O | ||
ATOM 22 O3 SER 3 11.233 9.084 -1.836 1.00 0.00 O1- | ||
ATOM 23 H SER 3 9.168 5.042 -0.389 1.00 0.00 H | ||
ATOM 24 HA SER 3 8.260 4.620 -3.166 1.00 0.00 H | ||
ATOM 25 HB1 SER 3 8.790 7.006 -3.164 1.00 0.00 H | ||
ATOM 26 HB2 SER 3 9.894 6.000 -4.252 1.00 0.00 H | ||
ATOM 27 N ALA 4 9.773 2.677 -2.627 1.00 0.00 N | ||
ATOM 28 CA ALA 4 10.719 1.563 -2.713 1.00 0.00 C | ||
ATOM 29 C ALA 4 10.123 0.422 -3.507 1.00 0.00 C | ||
ATOM 30 O ALA 4 10.604 0.050 -4.582 1.00 0.00 O | ||
ATOM 31 CB ALA 4 11.101 1.150 -1.277 1.00 0.00 C | ||
ATOM 32 O01 ALA 4 8.965 -0.245 -2.997 1.00 0.00 O1- | ||
ATOM 33 H ALA 4 8.784 2.472 -2.691 1.00 0.00 H | ||
ATOM 34 HA ALA 4 11.626 1.879 -3.258 1.00 0.00 H | ||
ATOM 35 1HB ALA 4 11.557 1.994 -0.721 1.00 0.00 H | ||
ATOM 36 2HB ALA 4 10.222 0.818 -0.694 1.00 0.00 H | ||
ATOM 37 3HB ALA 4 11.835 0.329 -1.266 1.00 0.00 H | ||
TER | ||
CONECT 1 2 10 11 12 | ||
CONECT 2 1 3 5 6 | ||
CONECT 3 2 4 13 | ||
CONECT 4 3 | ||
CONECT 5 2 7 8 9 | ||
CONECT 6 2 | ||
CONECT 7 5 | ||
CONECT 8 5 | ||
CONECT 9 5 | ||
CONECT 10 1 | ||
CONECT 11 1 | ||
CONECT 12 1 | ||
CONECT 13 3 14 23 | ||
CONECT 14 13 15 17 24 | ||
CONECT 15 14 16 27 | ||
CONECT 16 15 | ||
CONECT 17 14 18 25 26 | ||
CONECT 18 17 19 | ||
CONECT 19 18 20 21 22 | ||
CONECT 20 19 | ||
CONECT 21 19 | ||
CONECT 22 19 | ||
CONECT 23 13 | ||
CONECT 24 14 | ||
CONECT 25 17 | ||
CONECT 26 17 | ||
CONECT 27 15 28 33 | ||
CONECT 28 27 29 31 34 | ||
CONECT 29 28 30 32 | ||
CONECT 30 29 | ||
CONECT 31 28 35 36 37 | ||
CONECT 32 29 | ||
CONECT 33 27 | ||
CONECT 34 28 | ||
CONECT 35 31 | ||
CONECT 36 31 | ||
CONECT 37 31 | ||
END |
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doc/source/tutorials/6_adding_residues_links/files/force_fields/charmm/sep.rtp
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[ bondedtypes ] | ||
; Column 1 : default bondtype | ||
; Column 2 : default angletype | ||
; Column 3 : default proper dihedraltype | ||
; Column 4 : default improper dihedraltype | ||
; Column 5 : This controls the generation of dihedrals from the bonding. | ||
; All possible dihedrals are generated automatically. A value of | ||
; 1 here means that all these are retained. A value of | ||
; 0 here requires generated dihedrals be removed if | ||
; * there are any dihedrals on the same central atoms | ||
; specified in the residue topology, or | ||
; * there are other identical generated dihedrals | ||
; sharing the same central atoms, or | ||
; * there are other generated dihedrals sharing the | ||
; same central bond that have fewer hydrogen atoms | ||
; Column 6 : number of neighbors to exclude from non-bonded interactions | ||
; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms | ||
; 0 = do not generate such | ||
; Column 8 : 1 = remove proper dihedrals if found centered on the same | ||
; bond as an improper dihedral | ||
; 0 = do not generate such | ||
; bondtype angletype dihedraltype impropertype all_dih nrexcl HH14 bRemoveDih | ||
1 5 9 2 1 3 1 0 | ||
|
||
[ SEP ] | ||
[ atoms ] | ||
N N 0 0 | ||
HN H 0 1 | ||
CA C 0 2 | ||
HA H 0 3 | ||
CB C 0 4 | ||
HB1 H 0 5 | ||
HB2 H 0 6 | ||
OG O 0 7 | ||
C C 0 8 | ||
O O 0 9 | ||
P P 0 10 | ||
O1 O 0 11 | ||
O2 O 0 12 | ||
O3 O -1 13 | ||
[ bonds ] | ||
CB CA | ||
OG CB | ||
N HN | ||
N CA | ||
C CA | ||
C +N | ||
CA HA | ||
CB HB1 | ||
CB HB2 | ||
O C | ||
OG P | ||
P O1 | ||
P O2 | ||
P O3 | ||
|
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doc/source/tutorials/6_adding_residues_links/files/force_fields/martini3001/citations.bib
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@article{Martini3, | ||
abstract={The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein–protein and protein–lipid interactions and material science applications as ionic liquids and aedamers.}, | ||
author={Souza, Paulo C T and Alessandri, Riccardo and Barnoud, Jonathan and Thallmair, Sebastian and Faustino, Ignacio and Grünewald, Fabian and Patmanidis, Ilias and Abdizadeh, Haleh and Bruininks, Bart M H and Wassenaar, Tsjerk A and Kroon, Peter C and Melcr, Josef and Nieto, Vincent and Corradi, Valentina and Khan, Hanif M and Domański, Jan and Javanainen, Matti and Martinez-Seara, Hector and Reuter, Nathalie and Best, Robert B and Vattulainen, Ilpo and Monticelli, Luca and Periole, Xavier and Tieleman, D Peter and de Vries, Alex H and Marrink, Siewert J}, | ||
doi={10.1038/s41592-021-01098-3}, | ||
issn={1548-7105}, | ||
journal={Nature Methods}, | ||
title={{Martini 3: a general purpose force field for coarse-grained molecular dynamics}}, | ||
url={https://doi.org/10.1038/s41592-021-01098-3}, | ||
year={2021} | ||
} | ||
@article{Martini3smallmolecules, | ||
title={Martini 3 Coarse-Grained Force Field: Small Molecules}, | ||
author={Alessandri, Riccardo and Barnoud, Jonathan and Gertsen, Anders S and Patmanidis, Ilias and de Vries, Alex H and Souza, Paulo CT and Marrink, Siewert J}, | ||
journal={Advanced Theory and Simulations}, | ||
volume={5}, | ||
number={1}, | ||
pages={2100391}, | ||
year={2022}, | ||
publisher={Wiley Online Library} | ||
} |
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doc/source/tutorials/6_adding_residues_links/files/force_fields/martini3001/sep.ff
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;[ macros ] | ||
;protein_resnames "GLY|ALA|CYS|VAL|LEU|ILE|MET|PRO|HYP|ASN|GLN|ASP|ASPP|ASH|GLU|GLUP|GLH|THR|SER|LYS|LSN|LYN|ARG|HSE|HIS|HSD|HSP|HID|HIP|HIE|PHE|TYR|TRP|SEP" | ||
;protein_resnames_non_pro "GLY|ALA|CYS|VAL|LEU|ILE|MET|ASN|GLN|ASP|ASPP|ASH|GLU|GLUP|GLH|THR|SER|LYS|LSN|LYN|ARG|HSE|HIS|HSD|HSP|HID|HIP|HIE|PHE|TYR|TRP|SEP" | ||
;prot_default_bb_type P2 | ||
;stiff_fc 1000000 | ||
|
||
;;; PHOSPHOSERINE | ||
[ moleculetype ] | ||
SEP 1 | ||
|
||
[ warning ] | ||
THESE PARAMETERS ARE FOR DEMONSTRATION PURPOSES ONLY. DO NOT USE. | ||
|
||
[ atoms ] | ||
; id type resnr residue atom cgnr charge | ||
1 P2 1 SEP BB 1 0 | ||
2 Q5n 1 SEP SC1 1 -1 | ||
|
||
[ bonds ] | ||
BB SC1 1 0.33 5000 | ||
|
||
[ link ] | ||
[ warning ] | ||
THESE PARAMETERS ARE FOR DEMONSTRATION PURPOSES ONLY. DO NOT USE. | ||
[ atoms ] | ||
-BB {"resname": "ALA"} | ||
BB {"resname": "SEP"} | ||
SC1 {"resname": "SEP"} | ||
+BB {"resname": "ALA"} | ||
[ bonds ] | ||
BB +BB 1 0.35 4000 | ||
BB -BB 1 0.35 4000 | ||
[ angles ] | ||
-BB BB +BB 10 100 20 | ||
-BB BB SC1 2 100 25 |
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doc/source/tutorials/6_adding_residues_links/files/mappings/sep.charmm36.map
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[ molecule ] | ||
SEP | ||
|
||
[ from ] | ||
charmm | ||
|
||
[ to ] | ||
martini3001 | ||
|
||
[ martini ] | ||
BB SC1 | ||
|
||
[ mapping ] | ||
charmm | ||
|
||
[ atoms ] | ||
1 N BB | ||
2 HN BB | ||
3 CA BB | ||
4 HA !BB | ||
5 CB BB SC1 | ||
6 HB1 !SC1 | ||
7 HB2 !SC1 | ||
8 OG SC1 | ||
9 C BB | ||
10 O BB | ||
11 P SC1 | ||
12 O1 SC1 | ||
13 O2 SC1 | ||
14 O3 SC1 |
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76 changes: 76 additions & 0 deletions
76
doc/source/tutorials/7_adding_modifications/files/ala-sep-ala.pdb
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ATOM 1 N ALA 2 5.892 6.590 0.772 1.00 0.00 N1+ | ||
ATOM 2 CA ALA 2 6.787 5.479 0.424 1.00 0.00 C | ||
ATOM 3 C ALA 2 7.358 5.632 -0.971 1.00 0.00 C | ||
ATOM 4 O ALA 2 6.678 6.097 -1.907 1.00 0.00 O | ||
ATOM 5 CB ALA 2 6.008 4.158 0.573 1.00 0.00 C | ||
ATOM 6 HA ALA 2 7.626 5.500 1.145 1.00 0.00 H | ||
ATOM 7 1HB ALA 2 5.609 4.032 1.598 1.00 0.00 H | ||
ATOM 8 2HB ALA 2 5.143 4.107 -0.117 1.00 0.00 H | ||
ATOM 9 3HB ALA 2 6.644 3.281 0.368 1.00 0.00 H | ||
ATOM 10 H01 ALA 2 5.554 6.479 1.717 1.00 0.00 H | ||
ATOM 11 H02 ALA 2 6.398 7.464 0.706 1.00 0.00 H | ||
ATOM 12 H03 ALA 2 5.108 6.609 0.131 1.00 0.00 H | ||
ATOM 13 N SER 3 8.566 5.235 -1.183 1.00 0.00 N | ||
ATOM 14 CA SER 3 9.087 4.998 -2.535 1.00 0.00 C | ||
ATOM 15 C SER 3 10.146 3.913 -2.485 1.00 0.00 C | ||
ATOM 16 O SER 3 11.339 4.171 -2.285 1.00 0.00 O | ||
ATOM 17 CB SER 3 9.611 6.290 -3.232 1.00 0.00 C | ||
ATOM 18 OG SER 3 10.708 6.960 -2.686 1.00 0.00 O | ||
ATOM 19 P SER 3 10.949 7.716 -1.502 1.00 0.00 P | ||
ATOM 20 O1 SER 3 11.988 7.174 -0.832 1.00 0.00 O | ||
ATOM 21 O2 SER 3 9.680 8.015 -0.948 1.00 0.00 O | ||
ATOM 22 O3 SER 3 11.233 9.084 -1.836 1.00 0.00 O1- | ||
ATOM 23 H SER 3 9.168 5.042 -0.389 1.00 0.00 H | ||
ATOM 24 HA SER 3 8.260 4.620 -3.166 1.00 0.00 H | ||
ATOM 25 HB1 SER 3 8.790 7.006 -3.164 1.00 0.00 H | ||
ATOM 26 HB2 SER 3 9.894 6.000 -4.252 1.00 0.00 H | ||
ATOM 27 N ALA 4 9.773 2.677 -2.627 1.00 0.00 N | ||
ATOM 28 CA ALA 4 10.719 1.563 -2.713 1.00 0.00 C | ||
ATOM 29 C ALA 4 10.123 0.422 -3.507 1.00 0.00 C | ||
ATOM 30 O ALA 4 10.604 0.050 -4.582 1.00 0.00 O | ||
ATOM 31 CB ALA 4 11.101 1.150 -1.277 1.00 0.00 C | ||
ATOM 32 O01 ALA 4 8.965 -0.245 -2.997 1.00 0.00 O1- | ||
ATOM 33 H ALA 4 8.784 2.472 -2.691 1.00 0.00 H | ||
ATOM 34 HA ALA 4 11.626 1.879 -3.258 1.00 0.00 H | ||
ATOM 35 1HB ALA 4 11.557 1.994 -0.721 1.00 0.00 H | ||
ATOM 36 2HB ALA 4 10.222 0.818 -0.694 1.00 0.00 H | ||
ATOM 37 3HB ALA 4 11.835 0.329 -1.266 1.00 0.00 H | ||
TER | ||
CONECT 1 2 10 11 12 | ||
CONECT 2 1 3 5 6 | ||
CONECT 3 2 4 13 | ||
CONECT 4 3 | ||
CONECT 5 2 7 8 9 | ||
CONECT 6 2 | ||
CONECT 7 5 | ||
CONECT 8 5 | ||
CONECT 9 5 | ||
CONECT 10 1 | ||
CONECT 11 1 | ||
CONECT 12 1 | ||
CONECT 13 3 14 23 | ||
CONECT 14 13 15 17 24 | ||
CONECT 15 14 16 27 | ||
CONECT 16 15 | ||
CONECT 17 14 18 25 26 | ||
CONECT 18 17 19 | ||
CONECT 19 18 20 21 22 | ||
CONECT 20 19 | ||
CONECT 21 19 | ||
CONECT 22 19 | ||
CONECT 23 13 | ||
CONECT 24 14 | ||
CONECT 25 17 | ||
CONECT 26 17 | ||
CONECT 27 15 28 33 | ||
CONECT 28 27 29 31 34 | ||
CONECT 29 28 30 32 | ||
CONECT 30 29 | ||
CONECT 31 28 35 36 37 | ||
CONECT 32 29 | ||
CONECT 33 27 | ||
CONECT 34 28 | ||
CONECT 35 31 | ||
CONECT 36 31 | ||
CONECT 37 31 | ||
END |
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doc/source/tutorials/7_adding_modifications/files/force_fields/charmm/mods.ff
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[ modification ] | ||
SER-phos | ||
[ atoms ] | ||
O1 {"element": "O", "PTM_atom": true} | ||
O2 {"element": "O", "PTM_atom": true} | ||
O3 {"element": "O", "PTM_atom": true} | ||
P {"element": "P", "PTM_atom": true} | ||
OG {"element": "O"} | ||
HG1 {"element": "H", "replace": {"atomname": null}} | ||
[ edges ] | ||
OG P | ||
OG HG1 | ||
P O1 | ||
P O2 | ||
P O3 |
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doc/source/tutorials/7_adding_modifications/files/force_fields/martini3001/modification.ff
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[ modification ] | ||
SER-PO4 | ||
[ atoms ] | ||
BB {"PTM_atom": false} | ||
SC1 {"PTM_atom": false, "resname": "SER", "replace": {"atype": "Q5n", "charge": -1}} | ||
[ edges ] | ||
BB SC1 | ||
[ bonds ] | ||
BB SC1 1 0.33 5000 | ||
|
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