added martini3 modifications.ff and updated martini3 aminoacids.ff to…

… remove terminal modifications
marrink-lab · Jun 14, 2024 · eea3102 · eea3102
1 parent 76f491f
commit eea3102
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Showing 3 changed files with 38 additions and 62 deletions.
diff --git a/polyply/data/martini3/aminoacids.ff b/polyply/data/martini3/aminoacids.ff
@@ -802,64 +802,3 @@ resname $protein_resnames
 CA  BB
 [ edges ]
 CA BB
-
-[ link ]
-resname $protein_resnames
-[ atoms ]
-CA { }
-BB { }
-+BB { }
-[ exclusions ]
-#meta {"comment": "CA-BB"}
-CA +BB
-[ edges ]
-BB +BB
-
-;; Protein termini. These links should be applied last.
-[ link ]
-resname $protein_resnames
-[ atoms ]
-BB {"replace": {"atype": "Q5", "charge": 1}}
-[ non-edges ]
-BB -BB
-
-[ link ]
-resname $protein_resnames
-[ atoms ]
-BB {"replace": {"atype": "Q5", "charge": -1}}
-[ non-edges ]
-BB +BB
-
-[ link ]
-resname $protein_resnames
-[ atoms ]
-BB {"replace": {"atype": "P6", "charge": 0}}
-[ non-edges ]
-BB +BB
-BB -BB
-
-[ link ]
-resname $protein_resnames
-[ molmeta ]
-neutral_termini true
-[ atoms ]
-BB {"replace": {"atype": "P5", "charge": 0}}
-[ non-edges ]
-BB -BB
-
-[ link ]
-resname $protein_resnames
-[ molmeta ]
-neutral_termini true
-[ atoms ]
-BB {"replace": {"atype": "P6", "charge": 0}}
-[ non-edges ]
-BB +BB
-
-;; Cystein bridge
-[ link ]
-resname "CYS"
-[ constraints ]
-SC1 >SC1 1 0.24 {"comment": "Disulfide bridge"}
-[ features ]
-disulfide
diff --git a/polyply/data/martini3/modifications.ff b/polyply/data/martini3/modifications.ff
@@ -0,0 +1,37 @@
+[ citations ]
+Martini3
+
+[ modification ]
+C-ter
+[ atoms ]
+BB {"replace": {"atype": "Q5", "charge": -1.0}}
+
+[ modification ]
+N-ter
+[ atoms ]
+BB {"replace": {"atype": "Q5", "charge": 1.0}}
+
+[ modification ]
+zwitter
+[ atoms ]
+BB {"replace": {"atype": "Q5"}}
+
+[ modification ]
+COOH-ter
+[ atoms ]
+BB {"replace": {"atype": "P6", "charge": 0.0}}
+
+[ modification ]
+NH2-ter
+[ atoms ]
+BB {"replace": {"atype": "P6", "charge": 0.0}}
+
+[ modification ]
+CCAP-ter
+[ atoms ]
+BB {"replace": {"atype": "P1", "charge": 0.0}}
+
+[ modification ]
+NCAP-ter
+[ atoms ]
+BB {"replace": {"atype": "P2", "charge": 0.0}}
diff --git a/polyply/src/apply_termini.py b/polyply/src/apply_termini.py
@@ -54,7 +54,6 @@ def apply_terminal_mod(meta_molecule, term, res):
             # Raise some info about it so people know
             resname = meta_molecule.molecule.nodes[node]['resname']
             meta_molecule.molecule.nodes[node]['resname'] = resname + term[0]
-            LOGGER.info("Changing terminal resnames by their patch. Check your index file.")
 
             # add the modification from the modifications dict
             aname = meta_molecule.molecule.nodes[node]['atomname']
@@ -80,6 +79,7 @@ def prot_termini(meta_molecule):
     modifications = [('N-ter', 1),
                      ('C-ter', max_res)]
 
+    LOGGER.info("Changing terminal resnames by their patch. Check your index file.")
     for mod, res in modifications:
         meta_molecule = apply_terminal_mod(meta_molecule, mod, res)