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Merge pull request marrink-lab#591 from csbrasnett/idp-bugfix
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Idp bugfix
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@fgrunewald
fgrunewald authored Apr 27, 2024
2 parents cabacfd + d87d684 commit 7e359bd
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Showing 17 changed files with 1,073 additions and 4 deletions.
4 changes: 3 additions & 1 deletion bin/martinize2
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Expand Up @@ -444,7 +444,9 @@ def entry():
dest="ss",
type=str.upper,
metavar="SEQUENCE",
help=("Manually set the secondary " "structure of the proteins."),
help=("Manually set the secondary structure of the proteins. "
"Either give a dssp sequence for each residue in your input file "
"or a single letter to be repeated for the entire sequence, e.g. -ss C"),
)
secstruct_exclusion.add_argument(
"-collagen", action="store_true", default=False, help="Use collagen parameters"
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7 changes: 7 additions & 0 deletions vermouth/data/force_fields/martini3001/citations.bib
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Expand Up @@ -27,4 +27,11 @@ @article{MDTraj
pages={1528 -- 1532},
year={2015},
doi={10.1016/j.bpj.2015.08.015}
}
@article{M3_GO,
title={GōMartini 3: From large conformational changes in proteins to environmental bias corrections},
author={Souza, Paulo C. T. and Araujo, Luis P. Borges and Brasnett, Chris and Moreira, Rodrigo A. and Grunewald, Fabian and Park, Peter and Wang, Liguo and Razmazma, Hafez and Borges-Araujo, Ana C. and Cofas-Vargas, Luis F. and Monticelli, Luca and Mera-Adasme, Raul and Melo, Manuel N. and Wu, Sangwook and Marrink, Siewert J. and Poma, Adolfo B. and Thallmair, Sebastian},
url={https://www.biorxiv.org/content/10.1101/2024.04.15.589479v1},
doi={10.1101/2024.04.15.589479},
year={2024},
}
1 change: 1 addition & 0 deletions vermouth/processors/water_bias.py
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Expand Up @@ -89,6 +89,7 @@ def assign_residue_water_bias(self, molecule, res_graph):

if _in_resid_region(_old_resid, self.idr_regions):
eps = self.water_bias.get('idr', 0.0)
sec_struc = res_graph.nodes[res_node]['cgsecstruct']
elif self.auto_bias:
sec_struc = res_graph.nodes[res_node]['cgsecstruct']
eps = self.water_bias.get(sec_struc, 0.0)
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1 change: 1 addition & 0 deletions vermouth/rcsu/go_vs_includes.py
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Expand Up @@ -50,6 +50,7 @@ def run_molecule(self, molecule):

if not self.system:
raise ValueError('This processor requires a system.')
molecule.citations.add('M3_GO')

self.add_virtual_sites(molecule, prefix=moltype)

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8 changes: 8 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/hst5/README
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@@ -0,0 +1,8 @@
### DETAILS:

# Histidin 5 peptide, IDP

### TEST:

# -ff martini 3001
# BB-W bias for idr
423 changes: 423 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/hst5/aa.pdb
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154 changes: 154 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/cg.pdb
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ATOM 1 BB ASP 1 51.396 25.818 46.802 1.00 0.00
ATOM 2 SC1 ASP 1 53.604 28.123 47.334 1.00 0.00
ATOM 3 CA ASP 1 51.396 25.818 46.802 1.00 0.00
ATOM 4 BB SER 2 47.819 26.759 47.762 1.00 0.00
ATOM 5 SC1 SER 2 47.611 24.100 47.820 1.00 0.00
ATOM 6 CA SER 2 47.819 26.759 47.762 1.00 0.00
ATOM 7 BB HIS 3 48.614 29.420 49.220 1.00 0.00
ATOM 8 SC1 HIS 3 46.454 28.529 50.783 1.00 0.00
ATOM 9 SC2 HIS 3 44.587 26.928 50.901 1.00 0.00
ATOM 10 SC3 HIS 3 46.291 26.213 51.317 1.00 0.00
ATOM 11 CA HIS 3 48.614 29.420 49.220 1.00 0.00
ATOM 12 BB ALA 4 48.291 33.050 49.571 1.00 0.00
ATOM 13 SC1 ALA 4 50.214 32.984 48.343 1.00 0.00
ATOM 14 CA ALA 4 48.291 33.050 49.571 1.00 0.00
ATOM 15 BB LYS 5 48.324 36.494 51.046 1.00 0.00
ATOM 16 SC1 LYS 5 49.794 36.274 53.690 1.00 0.00
ATOM 17 SC2 LYS 5 51.827 36.685 56.075 1.00 0.00
ATOM 18 CA LYS 5 48.324 36.494 51.046 1.00 0.00
ATOM 19 BB ARG 6 48.796 37.672 48.646 1.00 0.00
ATOM 20 SC1 ARG 6 52.144 38.851 48.900 1.00 0.00
ATOM 21 SC2 ARG 6 55.436 38.203 47.910 1.00 0.00
ATOM 22 CA ARG 6 48.796 37.672 48.646 1.00 0.00
ATOM 23 BB HIS 7 47.357 39.686 45.649 1.00 0.00
ATOM 24 SC1 HIS 7 45.874 40.804 47.328 1.00 0.00
ATOM 25 SC2 HIS 7 44.240 40.977 49.126 1.00 0.00
ATOM 26 SC3 HIS 7 45.973 41.084 49.689 1.00 0.00
ATOM 27 CA HIS 7 47.357 39.686 45.649 1.00 0.00
ATOM 28 BB HIS 8 48.832 38.121 43.409 1.00 0.00
ATOM 29 SC1 HIS 8 51.039 39.429 43.608 1.00 0.00
ATOM 30 SC2 HIS 8 52.655 40.548 45.072 1.00 0.00
ATOM 31 SC3 HIS 8 51.656 41.617 43.892 1.00 0.00
ATOM 32 CA HIS 8 48.832 38.121 43.409 1.00 0.00
ATOM 33 BB GLY 9 46.667 37.663 40.263 1.00 0.00
ATOM 34 CA GLY 9 46.667 37.663 40.263 1.00 0.00
ATOM 35 BB TYR 10 44.378 39.639 41.126 1.00 0.00
ATOM 36 SC1 TYR 10 43.524 37.734 42.743 1.00 0.00
ATOM 37 SC2 TYR 10 45.004 36.493 44.400 1.00 0.00
ATOM 38 SC3 TYR 10 43.704 35.245 42.661 1.00 0.00
ATOM 39 SC4 TYR 10 45.202 33.915 44.249 1.00 0.00
ATOM 40 CA TYR 10 44.378 39.639 41.126 1.00 0.00
ATOM 41 BB LYS 11 42.597 41.909 39.147 1.00 0.00
ATOM 42 SC1 LYS 11 40.804 42.674 41.693 1.00 0.00
ATOM 43 SC2 LYS 11 38.391 43.469 43.698 1.00 0.00
ATOM 44 CA LYS 11 42.597 41.909 39.147 1.00 0.00
ATOM 45 BB ARG 12 43.974 42.129 36.009 1.00 0.00
ATOM 46 SC1 ARG 12 46.464 41.297 37.500 1.00 0.00
ATOM 47 SC2 ARG 12 48.901 42.948 36.475 1.00 0.00
ATOM 48 CA ARG 12 43.974 42.129 36.009 1.00 0.00
ATOM 49 BB LYS 13 41.530 42.801 34.539 1.00 0.00
ATOM 50 SC1 LYS 13 40.364 39.677 33.530 1.00 0.00
ATOM 51 SC2 LYS 13 39.333 36.588 33.068 1.00 0.00
ATOM 52 CA LYS 13 41.530 42.801 34.539 1.00 0.00
ATOM 53 BB PHE 14 39.614 45.182 32.015 1.00 0.00
ATOM 54 SC1 PHE 14 42.274 45.354 30.975 1.00 0.00
ATOM 55 SC2 PHE 14 44.618 46.260 31.553 1.00 0.00
ATOM 56 SC3 PHE 14 44.629 44.365 31.070 1.00 0.00
ATOM 57 CA PHE 14 39.614 45.182 32.015 1.00 0.00
ATOM 58 BB HIS 15 36.967 43.773 32.799 1.00 0.00
ATOM 59 SC1 HIS 15 36.939 43.654 29.968 1.00 0.00
ATOM 60 SC2 HIS 15 37.946 44.302 27.829 1.00 0.00
ATOM 61 SC3 HIS 15 38.658 42.813 28.653 1.00 0.00
ATOM 62 CA HIS 15 36.967 43.773 32.799 1.00 0.00
ATOM 63 BB GLU 16 33.927 42.551 33.628 1.00 0.00
ATOM 64 SC1 GLU 16 31.369 45.556 34.838 1.00 0.00
ATOM 65 CA GLU 16 33.927 42.551 33.628 1.00 0.00
ATOM 66 BB LYS 17 32.672 40.057 35.585 1.00 0.00
ATOM 67 SC1 LYS 17 34.991 39.371 38.010 1.00 0.00
ATOM 68 SC2 LYS 17 35.514 37.193 39.934 1.00 0.00
ATOM 69 CA LYS 17 32.672 40.057 35.585 1.00 0.00
ATOM 70 BB HIS 18 31.735 37.098 34.878 1.00 0.00
ATOM 71 SC1 HIS 18 31.389 37.119 32.093 1.00 0.00
ATOM 72 SC2 HIS 18 31.564 39.139 30.759 1.00 0.00
ATOM 73 SC3 HIS 18 31.363 37.536 29.813 1.00 0.00
ATOM 74 CA HIS 18 31.735 37.098 34.878 1.00 0.00
ATOM 75 BB HIS 19 29.310 34.719 36.500 1.00 0.00
ATOM 76 SC1 HIS 19 28.174 36.574 37.673 1.00 0.00
ATOM 77 SC2 HIS 19 27.189 38.700 37.147 1.00 0.00
ATOM 78 SC3 HIS 19 26.172 37.163 36.692 1.00 0.00
ATOM 79 CA HIS 19 29.310 34.719 36.500 1.00 0.00
ATOM 80 BB SER 20 29.061 32.049 34.708 1.00 0.00
ATOM 81 SC1 SER 20 29.567 33.108 32.540 1.00 0.00
ATOM 82 CA SER 20 29.061 32.049 34.708 1.00 0.00
ATOM 83 BB HIS 21 31.834 31.502 35.793 1.00 0.00
ATOM 84 SC1 HIS 21 33.089 30.564 33.583 1.00 0.00
ATOM 85 SC2 HIS 21 32.894 30.830 31.192 1.00 0.00
ATOM 86 SC3 HIS 21 32.541 29.131 31.878 1.00 0.00
ATOM 87 CA HIS 21 31.834 31.502 35.793 1.00 0.00
ATOM 88 BB ARG 22 33.233 29.738 38.283 1.00 0.00
ATOM 89 SC1 ARG 22 30.387 29.311 39.376 1.00 0.00
ATOM 90 SC2 ARG 22 26.801 30.117 38.020 1.00 0.00
ATOM 91 CA ARG 22 33.233 29.738 38.283 1.00 0.00
ATOM 92 BB GLY 23 35.664 31.392 39.242 1.00 0.00
ATOM 93 CA GLY 23 35.664 31.392 39.242 1.00 0.00
ATOM 94 BB TYR 24 38.870 32.826 38.137 1.00 0.00
ATOM 95 SC1 TYR 24 38.899 35.429 39.123 1.00 0.00
ATOM 96 SC2 TYR 24 38.604 37.120 37.271 1.00 0.00
ATOM 97 SC3 TYR 24 39.737 37.759 39.455 1.00 0.00
ATOM 98 SC4 TYR 24 39.515 39.477 37.519 1.00 0.00
ATOM 99 CA TYR 24 38.870 32.826 38.137 1.00 0.00
TER 100 TYR 24
CONECT 1 2 4
CONECT 4 5 7
CONECT 7 8 12
CONECT 8 9 10
CONECT 9 10
CONECT 12 13 15
CONECT 15 16 19
CONECT 16 17
CONECT 19 20 23
CONECT 20 21
CONECT 23 24 28
CONECT 24 25 26
CONECT 25 26
CONECT 28 29 33
CONECT 29 30 31
CONECT 30 31
CONECT 33 35
CONECT 35 36 41
CONECT 36 37 38
CONECT 37 38 39
CONECT 38 39
CONECT 41 42 45
CONECT 42 43
CONECT 45 46 49
CONECT 46 47
CONECT 49 50 53
CONECT 50 51
CONECT 53 54 58
CONECT 54 55 56
CONECT 55 56
CONECT 58 59 63
CONECT 59 60 61
CONECT 60 61
CONECT 63 64 66
CONECT 66 67 70
CONECT 67 68
CONECT 70 71 75
CONECT 71 72 73
CONECT 72 73
CONECT 75 76 80
CONECT 76 77 78
CONECT 77 78
CONECT 80 81 83
CONECT 83 84 88
CONECT 84 85 86
CONECT 85 86
CONECT 88 89 92
CONECT 89 90
CONECT 92 94
CONECT 94 95
CONECT 95 96 97
CONECT 96 97 98
CONECT 97 98
END
3 changes: 3 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/citation
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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

9 changes: 9 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/command
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martinize2
-f ../aa.pdb
-ff martini3001
-x cg.pdb
-o topol.top
-ss C
-water-bias
-water-bias-eps idr:0.5
-id-regions 1:24
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