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Add tutorial input files
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76 changes: 76 additions & 0 deletions 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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[ 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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@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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;[ 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
Original file line number Diff line number Diff line change
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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
16 changes: 9 additions & 7 deletions doc/source/tutorials/6_adding_residues_links/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@ serine residue (``OC(=O)C(N)COP(=O)(=O)[O-]``). Note that the parameters
presented here are for demonstration purposes only and not fit for actual
science or simulations!

All input files for this tutorial can be found on `github <https://github.com/marrink-lab/vermouth-martinize/tree/master/doc/source/tutorials/6_adding_residues_links/files>`_.

The input force field
---------------------
The input force field is the force field best describing the structure and atom
Expand All @@ -23,10 +25,10 @@ your input structure, only the atom names and edges are relevant.
We'll start by creating a force fields folder we can use to create the tutorial
files; and in that folder we need to create a force field named ``charmm``::

mkdir -p tutorial_ff/charmm
mkdir -p force_fields/charmm

Now we need to add the SEP :ref:`data:block` to our ``charmm`` folder. Let's
put it in the file ``tutorial_ff/charmm/sep.rtp``::
put it in the file ``force_fields/charmm/sep.rtp``::

[ bondedtypes ]
1 5 9 2 1 3 1 0
Expand Down Expand Up @@ -71,9 +73,9 @@ We also need to add the SEP :ref:`data:block` to the output force field. Of
course we'll use Martini 3 for this. Let's again start by making a martini3001
folder::

mkdir -p tutorial_ff/martini3001
mkdir -p force_fields/martini3001

Now to add the block to ``tutorial_ff/martini3001/sep.ff``::
Now to add the block to ``force_fields/martini3001/sep.ff``::

;;; PHOSPHOSERINE
[ moleculetype ]
Expand All @@ -88,7 +90,7 @@ Now to add the block to ``tutorial_ff/martini3001/sep.ff``::
[ bonds ]
BB SC1 1 0.33 5000

At this point we can run ``martinize2 -ff-dir tutorial_ff -list-blocks`` to
At this point we can run ``martinize2 -ff-dir force_fields -list-blocks`` to
check whether our new SEP blocks are picked up.

The mapping
Expand Down Expand Up @@ -137,7 +139,7 @@ CB will contribute to BB and SC1 with equal weight.

Ok, this great! At this point we can run ``martinize2``::

martinize2 -ff-dir tutorial_ff -map-dir mappings -f ala-sep-ala.pdb -x AJA.pdb -o topol.top
martinize2 -ff-dir force_fields -map-dir mappings -f ala-sep-ala.pdb -x AJA.pdb -o topol.top

And inspect the resulting ``molecule_0.itp`` to make sure our final topology is
correct::
Expand Down Expand Up @@ -182,7 +184,7 @@ In Vermouth and martinize2 we use :ref:`links <data:link>` to describe interacti
between residues. We need to these to the output force field---in this case
martini3001.

We can add the following to ``tutorial_ff/martini3001/sep.ff``::
We can add the following to ``force_fields/martini3001/sep.ff``::

[ link ]
[ bonds ]
Expand Down
76 changes: 76 additions & 0 deletions 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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[ 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
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
[ 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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