marrink-lab · pckroon · Sep 3, 2020 · Jun 10, 2020 · Jun 10, 2020 · Jun 10, 2020
diff --git a/bin/martinize2 b/bin/martinize2
@@ -354,7 +354,7 @@ def entry():
                           help='Write elastic bonds')
     rb_group.add_argument('-ef', dest='rb_force_constant', type=float, default=500,
                           help='Elastic bond force constant Fc in kJ/mol/nm^2')
-    rb_group.add_argument('-el', dest='rb_lower_bound', type=float, default=0.5,
+    rb_group.add_argument('-el', dest='rb_lower_bound', type=float, default=0,
                           help='Elastic bond lower cutoff: F = Fc if rij < lo')
     rb_group.add_argument('-eu', dest='rb_upper_bound', type=float, default=0.9,
                           help='Elastic bond upper cutoff: F = 0  if rij > up')
@@ -364,7 +364,7 @@ def entry():
                           default=None)
     rb_group.add_argument('-ea', dest='rb_decay_factor', type=float, default=0,
                           help='Elastic bond decay factor a')
-    rb_group.add_argument('-ep', dest='rb_decay_power', type=float, default=0,
+    rb_group.add_argument('-ep', dest='rb_decay_power', type=float, default=1,
                           help='Elastic bond decay power p')
     rb_group.add_argument('-em', dest='rb_minimum_force', type=float, default=0,
                           help='Remove elastic bonds with force constant lower than this')
@@ -706,6 +706,7 @@ def entry():
 
     # TODO: allow ignoring warnings per class/amount (i.e. ignore 2
     #       inconsistent-data warnings)
+
     number_of_warnings = COUNTER.number_of_counts_by(level=logging.WARNING)
     if args.maxwarn < number_of_warnings:
         LOGGER.error('{} warnings were encountered. No output files will be '

diff --git a/vermouth/data/force_fields/elnedyn22/modifications.ff b/vermouth/data/force_fields/elnedyn22/modifications.ff
@@ -22,3 +22,8 @@ BB {"replace": {"atype": "P5", "charge": 0}}
 NH2-ter
 [ atoms ]
 BB {"replace": {"atype": "P5", "charge": 0}}
+
+[ modification ]
+ASP0
+[ atoms ]
+SC1 {"resname": "ASP", "replace": {"atype": "P3", "charge": 0}}
diff --git a/vermouth/data/force_fields/martini30b32/aminoacids.ff b/vermouth/data/force_fields/martini30b32/aminoacids.ff
@@ -738,27 +738,6 @@ BB ++BB 1 0.640 2500
 +BB +++BB 1 0.640 2500
 BB +++BB 1 0.970 2500
 
-;; Protein terminii. These links should be applied last.
-[ link ]
-[ molmeta ]
-neutral_termini not(true)
-[ features ]
-neutral_termini
-[ atoms ]
-BB {"replace": {"atype": "Qp", "charge": 1}}
-[ non-edges ]
-BB -BB
-
-[ link ]
-[ molmeta ]
-neutral_termini not(true)
-[ features ]
-neutral_termini
-[ atoms ]
-BB {"replace": {"atype": "Qn", "charge": -1}}
-[ non-edges ]
-BB +BB
-
 ;; Cystein bridge
 [ link ]
 resname "CYS"

diff --git a/vermouth/data/force_fields/martini30b32/modifications.ff b/vermouth/data/force_fields/martini30b32/modifications.ff
@@ -0,0 +1,10 @@
+[ modification ]
+C-ter
+[ atoms ]
+BB {"replace": {"atype": "Qn", "charge": -1}}
+
+[ modification ]
+N-ter
+[ atoms ]
+BB {"replace": {"atype": "Qp", "charge": 1}}
+
diff --git a/vermouth/data/force_fields/martini30dev/aminoacids.ff b/vermouth/data/force_fields/martini30dev/aminoacids.ff
@@ -817,43 +817,6 @@ BB ++BB 1 0.640 2500
 +BB +++BB 1 0.640 2500
 BB +++BB 1 0.970 2500
 
-;; Protein terminii. These links should be applied last.
-[ link ]
-[ molmeta ]
-neutral_termini not(true)
-[ features ]
-neutral_termini
-[ atoms ]
-BB {"replace": {"atype": "Q1", "charge": 1}}
-[ non-edges ]
-BB -BB
-
-[ link ]
-[ molmeta ]
-neutral_termini not(true)
-[ atoms ]
-BB {"replace": {"atype": "Q1", "charge": -1}}
-[ non-edges ]
-BB +BB
-
-[ link ]
-[ molmeta ]
-neutral_termini true
-[ atoms ]
-BB {"replace": {"atype": "P4"}}
-[ non-edges ]
-BB -BB
-
-[ link ]
-[ molmeta ]
-neutral_termini true
-[ features ]
-neutral_termini
-[ atoms ]
-BB {"replace": {"atype": "P5"}}
-[ non-edges ]
-BB +BB
-
 ;; Cystein bridge
 [ link ]
 resname "CYS"

diff --git a/vermouth/data/force_fields/martini30dev/modifications.ff b/vermouth/data/force_fields/martini30dev/modifications.ff
@@ -0,0 +1,19 @@
+[ modification ]
+C-ter
+[ atoms ]
+BB {"replace": {"atype": "Q1", "charge": -1}}
+
+[ modification ]
+N-ter
+[ atoms ]
+BB {"replace": {"atype": "Q1", "charge": 1}}
+
+[ modification ]
+COOH-ter
+[ atoms ]
+BB {"replace": {"atype": "P5", "charge": 0}}
+
+[ modification ]
+NH2-ter
+[ atoms ]
+BB {"replace": {"atype": "P4", "charge": 0}}
diff --git a/vermouth/data/mappings/elnedyn/elnedyn22/modifications.mapping b/vermouth/data/mappings/elnedyn/elnedyn22/modifications.mapping
@@ -105,3 +105,28 @@ N   BB 0
 CA  BB
 C   BB 0
 O   BB 0
+
+
+[modification]
+[ from ]
+universal
+[ to ]
+elnedyn22
+[ from blocks ]
+ASP0
+[ to blocks ]
+ASP0
+[ from nodes ]
+CB
+CG
+OD1
+[ from edges ]
+CB CG
+CG OD1
+CG OD2
+[ mapping ]
+CB SC1
+CG SC1
+OD1 SC1
+OD2 SC1
+HD2 SC1
diff --git a/vermouth/data/mappings/martini30/modifications.mapping b/vermouth/data/mappings/martini30/modifications.mapping
@@ -0,0 +1,150 @@
+[ modification ]
+[ from ]
+universal
+[ to ]
+martini30b32
+
+[ from blocks ]
+C-ter
+[ to blocks ]
+C-ter
+
+[ from nodes ]
+N
+HN
+
+[ from edges ]
+HN N
+N CA
+
+[ mapping ]
+CA BB
+C  BB
+O  BB
+OXT BB
+
+
+[modification]
+[ from ]
+universal
+[ to ]
+martini30b32
+[ from blocks ]
+N-ter
+[ to blocks ]
+N-ter
+
+[ from nodes ]
+C
+O
+
+[ from edges ]
+C O
+CA C
+
+[ mapping ]
+HN1 BB
+HN2 BB
+HN3 BB
+N   BB
+CA  BB
+C   BB
+O   BB
+
+;#################
+;# Martini 30dev #
+;#################
+
+[ modification ]
+[ from ]
+universal
+[ to ]
+martini30dev
+[ from blocks ]
+C-ter
+[ to blocks ]
+C-ter
+[ from nodes ]
+N
+HN
+[ from edges ]
+HN N
+N CA
+[ mapping ]
+CA BB
+C  BB
+O  BB
+OXT BB
+
+
+[modification]
+[ from ]
+universal
+[ to ]
+martini30dev
+[ from blocks ]
+N-ter
+[ to blocks ]
+N-ter
+[ from nodes ]
+C
+O
+[ from edges ]
+C O
+CA C
+[ mapping ]
+HN1 BB
+HN2 BB
+HN3 BB
+N   BB
+CA  BB
+C   BB
+O   BB
+
+[ modification ]
+[ from ]
+universal
+[ to ]
+martini30dev
+[ from blocks ]
+COOH-ter
+[ to blocks ]
+COOH-ter
+[ from nodes ]
+N
+HN
+[ from edges ]
+HN N
+N CA
+[ mapping ]
+HN BB
+N BB
+CA BB
+C  BB
+O  BB
+HO BB
+OXT BB
+
+
+[modification]
+[ from ]
+universal
+[ to ]
+martini30dev
+[ from blocks ]
+NH2-ter
+[ to blocks ]
+NH2-ter
+[ from nodes ]
+C
+O
+[ from edges ]
+C O
+CA C
+[ mapping ]
+HN1 BB
+HN2 BB
+N   BB
+CA  BB
+C   BB
+O   BB
diff --git a/vermouth/gmx/__init__.py b/vermouth/gmx/__init__.py
@@ -19,4 +19,5 @@
 
 from .gro import read_gro, write_gro
 from .itp import write_molecule_itp
+from .itp_read import read_itp
 from .rtp import read_rtp
diff --git a/vermouth/pdb/pdb.py b/vermouth/pdb/pdb.py
@@ -522,8 +522,8 @@ def write_pdb_string(system, conect=True, omit_charges=True, nan_missing_pos=Fal
         format_string = 'CONECT '
         for mol_idx, molecule in enumerate(system.molecules):
             for node_idx in molecule:
-                todo = [nodeidx2atomid[(mol_idx, n_idx)]
-                        for n_idx in molecule[node_idx] if n_idx > node_idx]
+                todo = sorted(nodeidx2atomid[(mol_idx, n_idx)]
+                              for n_idx in molecule[node_idx] if n_idx > node_idx)
                 while todo:
                     current, todo = todo[:4], todo[4:]
                     fmt = ['CONECT'] + [number_fmt]*(len(current) + 1)

diff --git a/vermouth/processors/locate_charge_dummies.py b/vermouth/processors/locate_charge_dummies.py
@@ -58,9 +58,8 @@ def colinear_pair():
     """
     vector = np.random.rand(3)
     vector /= np.linalg.norm(vector)
-    vector *= 2
     points = np.stack([np.zeros((3, )), vector])
-    points -= points / 2
+    points -= vector/2
     return points
 
 
@@ -193,7 +192,6 @@ def locate_all_dummies(molecule, attribute_tag=DEFAULT_DUMMY_ATTRIBUTE):
         dummy_keys = [pair[1] for pair in dummy_pairs]
         locate_dummy(molecule, anchor_key, dummy_keys, attribute_tag)
 
-
 class LocateChargeDummies(Processor):
     def __init__(self, attribute_tag=DEFAULT_DUMMY_ATTRIBUTE):
         super().__init__()

diff --git a/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/README b/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/README
@@ -0,0 +1,12 @@
+### DETAILS: 
+
+# Original PDB CODE: 1ICO 
+# Structure from NMR experiment: select the first model to martinize
+# Replace the residue name DPR (d-proline, residue 8) and DAL (d-alanine, residue 23) for PRO and ALA
+# Maybe could be used to test d- amino acids
+
+### TEST: 
+
+# -ff martini22
+# -cys auto
+# -dssp