Adapt martini3 FF files to overlap the appropriate angles for scFix

marrink-lab · May 6, 2024 · 7b86c29 · 7b86c29
1 parent 88e9cbd
commit 7b86c29
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Showing 3 changed files with 69 additions and 30 deletions.
diff --git a/vermouth/data/force_fields/martini3001/aminoacids.ff b/vermouth/data/force_fields/martini3001/aminoacids.ff
@@ -944,6 +944,19 @@ scfix true
 [ non-edges ]
 BB SC1
 
+[ link ]
+resname $protein_resnames
+[ angles ]
+-BB  BB  SC1  2 100 25 {"group": "BBS angles regular martini", "version": 1}
+
+[ link ]
+resname $protein_resnames
+[ angles ]
+#meta {"group": "First SBB regular martini"}
+SC1 BB +BB 2 100 25 {"version": 1}
+[ non-edges ]
+BB -BB
+
 [ link ]
 resname $protein_resnames
 [ features ]
@@ -960,20 +973,20 @@ scfix
 [ molmeta ]
 scfix true
 [ angles ]
-BB +BB +SC1 10 100 15 {"group": "SC-BB-BB and BB-BB-SC scFix", "comment": "BB-BB-SC"}
-
-[ link ]
-resname $protein_resnames
-[ angles ]
--BB  BB  SC1  2 100 25 {"group": "BBS angles regular martini", "version": 1}
+SC1 BB +BB 10 100 15 {"group": "SC-BB-BB and BB-BB-SC scFix", "comment": "SC-BB-BB"}
+SC1 BB +BB 2 100 25 {"version": 1, "group": "First SBB regular martini"}
+[ non-edges ]
+BB -BB
 
 [ link ]
 resname $protein_resnames
+[ features ]
+scfix
+[ molmeta ]
+scfix true
 [ angles ]
-#meta {"group": "First SBB regular martini"}
-SC1 BB +BB 2 100 25 {"version": 1}
-[ non-edges ]
-BB -BB
+BB +BB +SC1  2 100 25 {"group": "BBS angles regular martini", "version": 1}
+BB +BB +SC1 10 100 15 {"group": "SC-BB-BB and BB-BB-SC scFix", "comment": "BB-BB-SC"}
 
 ;; Links for the different secondary structures.
 ;; Setup the bonds. We only have the bonds assuming everything is coil.

diff --git a/vermouth/data/force_fields/martini30b32/aminoacids.ff b/vermouth/data/force_fields/martini30b32/aminoacids.ff
@@ -530,6 +530,19 @@ scfix true
 #meta {"group": "SC-BB-BB-SC scFix"}
 SC1 BB +BB +SC1 1 dihphase(SC1,BB,+BB,+SC1|.0f) 75 1
 
+[ link ]
+resname $protein_resnames
+[ angles ]
+-BB  BB  SC1  2 100 25 {"group": "BBS angles regular martini", "version": 1}
+
+[ link ]
+resname $protein_resnames
+[ angles ]
+#meta {"group": "First SBB regular martini"}
+SC1 BB +BB 2 100 25 {"version": 1}
+[ non-edges ]
+BB -BB
+
 [ link ]
 resname $protein_resnames
 [ features ]
@@ -546,20 +559,20 @@ scfix
 [ molmeta ]
 scfix true
 [ angles ]
-BB +BB +SC1 10 100 15 {"group": "SC-BB-BB and BB-BB-SC scFix", "comment": "BB-BB-SC"}
-
-[ link ]
-resname $protein_resnames
-[ angles ]
--BB  BB  SC1  2 100 25 {"group": "BBS angles regular martini", "version": 1}
+SC1 BB +BB 10 100 15 {"group": "SC-BB-BB and BB-BB-SC scFix", "comment": "SC-BB-BB"}
+SC1 BB +BB 2 100 25 {"version": 1, "group": "First SBB regular martini"}
+[ non-edges ]
+BB -BB
 
 [ link ]
 resname $protein_resnames
+[ features ]
+scfix
+[ molmeta ]
+scfix true
 [ angles ]
-#meta {"group": "First SBB regular martini"}
-SC1 BB +BB 2 100 25 {"version": 1}
-[ non-edges ]
-BB -BB
+BB +BB +SC1  2 100 25 {"group": "BBS angles regular martini", "version": 1}
+BB +BB +SC1 10 100 15 {"group": "SC-BB-BB and BB-BB-SC scFix", "comment": "BB-BB-SC"}
 
 ;; Links for the different secondary structures.
 ;; Setup the bonds. We only have the bonds assuming everything is coil.

diff --git a/vermouth/data/force_fields/martini30dev/aminoacids.ff b/vermouth/data/force_fields/martini30dev/aminoacids.ff
@@ -575,6 +575,19 @@ scfix true
 #meta {"group": "SC-BB-BB-SC scFix"}
 SC1 BB +BB +SC1 1 dihphase(SC1,BB,+BB,+SC1|.0f) 75 1
 
+[ link ]
+resname $protein_resnames
+[ angles ]
+-BB  BB  SC1  2 100 25 {"group": "BBS angles regular martini", "version": 1}
+
+[ link ]
+resname $protein_resnames
+[ angles ]
+#meta {"group": "First SBB regular martini"}
+SC1 BB +BB 2 100 25 {"version": 1}
+[ non-edges ]
+BB -BB
+
 [ link ]
 resname $protein_resnames
 [ features ]
@@ -591,20 +604,20 @@ scfix
 [ molmeta ]
 scfix true
 [ angles ]
-BB +BB +SC1 10 100 15 {"group": "SC-BB-BB and BB-BB-SC scFix", "comment": "BB-BB-SC"}
-
-[ link ]
-resname $protein_resnames
-[ angles ]
--BB  BB  SC1  2 100 25 {"group": "BBS angles regular martini", "version": 1}
+SC1 BB +BB 10 100 15 {"group": "SC-BB-BB and BB-BB-SC scFix", "comment": "SC-BB-BB"}
+SC1 BB +BB 2 100 25 {"version": 1, "group": "First SBB regular martini"}
+[ non-edges ]
+BB -BB
 
 [ link ]
 resname $protein_resnames
+[ features ]
+scfix
+[ molmeta ]
+scfix true
 [ angles ]
-#meta {"group": "First SBB regular martini"}
-SC1 BB +BB 2 100 25 {"version": 1}
-[ non-edges ]
-BB -BB
+BB +BB +SC1  2 100 25 {"group": "BBS angles regular martini", "version": 1}
+BB +BB +SC1 10 100 15 {"group": "SC-BB-BB and BB-BB-SC scFix", "comment": "BB-BB-SC"}
 
 ;; Links for the different secondary structures.
 ;; Setup the bonds. We only have the bonds assuming everything is coil.