Merge pull request #476 from marrink-lab/PRO-c-ter

Proline termini mappings
marrink-lab · Nov 4, 2022 · 29bc3d5 · 29bc3d5
2 parents d2f38f9 + 8831675
commit 29bc3d5
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diff --git a/vermouth/data/mappings/martini3001/modifications.charmm36.mapping b/vermouth/data/mappings/martini3001/modifications.charmm36.mapping
@@ -11,10 +11,8 @@ C-ter
 
 [ from nodes ]
 N
-HN
 
 [ from edges ]
-HN N
 N CA
 
 [ mapping ]
@@ -63,14 +61,11 @@ COOH-ter
 
 [ from nodes ]
 N
-HN
 
 [ from edges ]
-HN N
 N CA
 
 [ mapping ]
-HN BB
 N BB
 CA BB
 C  BB

diff --git a/vermouth/tests/data/integration_tests/tier-0/dipro-termini/README b/vermouth/tests/data/integration_tests/tier-0/dipro-termini/README
@@ -0,0 +1 @@
+# Test with a PRO-PRO dipeptide to make sure neutral termini can be applied to proline
diff --git a/vermouth/tests/data/integration_tests/tier-0/dipro-termini/aa.pdb b/vermouth/tests/data/integration_tests/tier-0/dipro-termini/aa.pdb
@@ -0,0 +1,62 @@
+ATOM      1  N   PRO     2       0.649  -0.549   1.064  1.00  0.00           N  
+ATOM      2  CA  PRO     2       1.159   0.454   0.141  1.00  0.00           C  
+ATOM      3  C   PRO     2       1.064   1.870   0.735  1.00  0.00           C  
+ATOM      4  O   PRO     2       0.038   2.239   1.307  1.00  0.00           O  
+ATOM      5  CB  PRO     2       0.249   0.252  -1.080  1.00  0.00           C  
+ATOM      6  CG  PRO     2      -1.068  -0.252  -0.471  1.00  0.00           C  
+ATOM      7  CD  PRO     2      -0.604  -1.157   0.674  1.00  0.00           C  
+ATOM      8  HA  PRO     2       2.202   0.248  -0.110  1.00  0.00           H  
+ATOM      9 2HB  PRO     2       0.674  -0.529  -1.713  1.00  0.00           H  
+ATOM     10 3HB  PRO     2       0.122   1.162  -1.671  1.00  0.00           H  
+ATOM     11 2HG  PRO     2      -1.687  -0.787  -1.194  1.00  0.00           H  
+ATOM     12 3HG  PRO     2      -1.629   0.591  -0.063  1.00  0.00           H  
+ATOM     13 2HD  PRO     2      -0.421  -2.174   0.318  1.00  0.00           H  
+ATOM     14 3HD  PRO     2      -1.313  -1.168   1.504  1.00  0.00           H  
+ATOM     15  N   PRO     3       2.065   2.676   0.631  1.00  0.00           N  
+ATOM     16  CA  PRO     3       2.041   4.028   1.170  1.00  0.00           C  
+ATOM     17  C   PRO     3       1.097   4.940   0.368  1.00  0.00           C  
+ATOM     18  O   PRO     3       0.469   4.496  -0.594  1.00  0.00           O  
+ATOM     19  CB  PRO     3       3.516   4.441   1.055  1.00  0.00           C  
+ATOM     20  CG  PRO     3       4.021   3.647  -0.159  1.00  0.00           C  
+ATOM     21  CD  PRO     3       3.298   2.304  -0.028  1.00  0.00           C  
+ATOM     22  H01 PRO     3       1.032   6.867  -0.035  1.00  0.00           H  
+ATOM     23  O01 PRO     3       0.947   6.312   0.743  1.00  0.00           O  
+ATOM     24  HA  PRO     3       1.718   4.019   2.214  1.00  0.00           H  
+ATOM     25 2HB  PRO     3       4.048   4.108   1.949  1.00  0.00           H  
+ATOM     26 3HB  PRO     3       3.648   5.519   0.942  1.00  0.00           H  
+ATOM     27 2HG  PRO     3       5.107   3.532  -0.162  1.00  0.00           H  
+ATOM     28 3HG  PRO     3       3.703   4.143  -1.078  1.00  0.00           H  
+ATOM     29 2HD  PRO     3       3.860   1.618   0.609  1.00  0.00           H  
+ATOM     30 3HD  PRO     3       3.102   1.845  -1.000  1.00  0.00           H  
+TER   
+CONECT    1    2    7
+CONECT    2    1    3    5    8
+CONECT    3    2    4   15
+CONECT    4    3
+CONECT    5    2    6    9   10
+CONECT    6    5    7   11   12
+CONECT    7    1    6   13   14
+CONECT    8    2
+CONECT    9    5
+CONECT   10    5
+CONECT   11    6
+CONECT   12    6
+CONECT   13    7
+CONECT   14    7
+CONECT   15    3   16   21
+CONECT   16   15   17   19   24
+CONECT   17   16   18   23
+CONECT   18   17
+CONECT   19   16   20   25   26
+CONECT   20   19   21   27   28
+CONECT   21   15   20   29   30
+CONECT   22   23
+CONECT   23   17   22
+CONECT   24   16
+CONECT   25   19
+CONECT   26   19
+CONECT   27   20
+CONECT   28   20
+CONECT   29   21
+CONECT   30   21
+END
diff --git a/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/cg.pdb b/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/cg.pdb
@@ -0,0 +1,8 @@
+ATOM      1 BB   PRO     1       0.674   1.038   0.858  1.00  0.00              
+ATOM      2 SC1  PRO     1      -0.474  -0.386  -0.292  1.00  0.00              
+ATOM      3 BB   PRO     2       1.271   4.576   0.417  1.00  0.00              
+ATOM      4 SC1  PRO     2       3.612   3.464   0.289  1.00  0.00              
+TER       5      PRO     2 
+CONECT    1    2    3
+CONECT    3    4
+END   
diff --git a/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/citation b/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/citation
@@ -0,0 +1 @@
+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
diff --git a/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command b/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command
@@ -0,0 +1,6 @@
+martinize2
+-f ../aa.pdb
+-x cg.pdb
+-o topol.top
+-ff martini3001
+-nt
diff --git a/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/molecule_0.itp
@@ -0,0 +1,31 @@
+; This file was generated using the following command:
+; /homes/peterkroon/virtualenvs/martinize2/bin/martinize2 -f ../aa.pdb -x cg.pdb -o topol.top -ff martini3001 -nt
+; martinize with vermouth 0.7.4.dev121
+
+; 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 P6  1 PRO BB  1   0 
+2 SC3 1 PRO SC1 2 0.0 
+3 P6  2 PRO BB  3   0 
+4 SC3 2 PRO SC1 4 0.0 
+
+[ bonds ]
+; Backbone bonds
+1 3 1 0.350 4000
+
+; Side chain bonds
+1 2 1 0.330 7500
+3 4 1 0.330 7500
+
+[ angles ]
+; BBS angles regular martini
+1 3 4 2 100 25
+
+; First SBB regular martini
+2 1 3 2 100 25
+
diff --git a/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/topol.top b/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/topol.top
@@ -0,0 +1,9 @@
+
+#include "martini.itp"
+#include "molecule_0.itp"
+
+[ system ]
+Title of the system
+
+[ molecules ]
+molecule_0    1
diff --git a/vermouth/tests/integration_tests/test_integration.py b/vermouth/tests/integration_tests/test_integration.py
@@ -128,6 +128,7 @@ def _interaction_equal(interaction1, interaction2):
     ['tier-0', 'mini-protein1_betasheet'],
     ['tier-0', 'mini-protein2_helix'],
     ['tier-0', 'mini-protein3_trp-cage'],
+    ['tier-0', 'dipro-termini'],
     ['tier-1', 'bpti'],
     ['tier-1', 'lysozyme'],
     ['tier-1', 'lysozyme_prot'],