From 05efeff756b9241e89ef1dd29d5033b7810c7a23 Mon Sep 17 00:00:00 2001
From: Erik Lindahl <erik@kth.se>
Date: Mon, 23 Jun 2014 02:34:37 +0200
Subject: [PATCH] Fixed GROMOS assignment of PRO-NH terminus torsions

This patch also adjusts the parameters for torsions
over N-CA bonds in the termini, according to
suggestions by Justin Lemkul & Drazen Petrov.

Fixes #1022.

Change-Id: Ib00d69eeddf924b1e7e2de33475d774d7da54899
---
 share/top/gromos43a1.ff/aminoacids.n.tdb | 10 ++++++----
 share/top/gromos43a2.ff/aminoacids.n.tdb | 10 ++++++----
 share/top/gromos53a5.ff/aminoacids.n.tdb | 10 ++++++----
 share/top/gromos53a6.ff/aminoacids.n.tdb | 10 ++++++----
 share/top/gromos54a7.ff/aminoacids.n.tdb | 10 ++++++----
 5 files changed, 30 insertions(+), 20 deletions(-)

diff --git a/share/top/gromos43a1.ff/aminoacids.n.tdb b/share/top/gromos43a1.ff/aminoacids.n.tdb
index 7b513a1fab..d14447ec33 100644
--- a/share/top/gromos43a1.ff/aminoacids.n.tdb
+++ b/share/top/gromos43a1.ff/aminoacids.n.tdb
@@ -21,7 +21,7 @@ CA	N	H1	ga_10
 CA	N	H2	ga_10
 CA	N	H3	ga_10
 [ dihedrals ]
-H1	N	CA	C	gd_14
+H1	N	CA	C	gd_19
 
 [ NH2 ]
 [ replace ]
@@ -39,7 +39,7 @@ H1	N	H2	ga_9
 CA	N	H1	ga_10
 CA	N	H2	ga_10
 [ dihedrals ]
-H1	N	CA	C	gd_14
+H1	N	CA	C	gd_19
 
 [ PRO-NH2+ ]
 [ replace ]
@@ -57,7 +57,7 @@ CA	N	H2	ga_10
 CD	N	H1	ga_10
 CD	N	H2	ga_10
 [ dihedrals ]
-H1	N	CA	C	gd_14
+CD	N	CA	C	gd_19
 
 [ PRO-NH ]
 [ replace ]
@@ -70,6 +70,8 @@ N	H	gb_2
 [ angles ]
 CA	N	H	ga_10
 CD	N	H	ga_10
+[ dihedrals ]
+CD      N       CA      C       gd_19
 
 [ GLY-NH3+ ]
 [ replace ]
@@ -92,5 +94,5 @@ CA	N	H1	ga_10
 CA	N	H2	ga_10
 CA	N	H3	ga_10
 [ dihedrals ]
-H1	N	CA	C	gd_14
+H1	N	CA	C	gd_19
 
diff --git a/share/top/gromos43a2.ff/aminoacids.n.tdb b/share/top/gromos43a2.ff/aminoacids.n.tdb
index 7b513a1fab..d14447ec33 100644
--- a/share/top/gromos43a2.ff/aminoacids.n.tdb
+++ b/share/top/gromos43a2.ff/aminoacids.n.tdb
@@ -21,7 +21,7 @@ CA	N	H1	ga_10
 CA	N	H2	ga_10
 CA	N	H3	ga_10
 [ dihedrals ]
-H1	N	CA	C	gd_14
+H1	N	CA	C	gd_19
 
 [ NH2 ]
 [ replace ]
@@ -39,7 +39,7 @@ H1	N	H2	ga_9
 CA	N	H1	ga_10
 CA	N	H2	ga_10
 [ dihedrals ]
-H1	N	CA	C	gd_14
+H1	N	CA	C	gd_19
 
 [ PRO-NH2+ ]
 [ replace ]
@@ -57,7 +57,7 @@ CA	N	H2	ga_10
 CD	N	H1	ga_10
 CD	N	H2	ga_10
 [ dihedrals ]
-H1	N	CA	C	gd_14
+CD	N	CA	C	gd_19
 
 [ PRO-NH ]
 [ replace ]
@@ -70,6 +70,8 @@ N	H	gb_2
 [ angles ]
 CA	N	H	ga_10
 CD	N	H	ga_10
+[ dihedrals ]
+CD      N       CA      C       gd_19
 
 [ GLY-NH3+ ]
 [ replace ]
@@ -92,5 +94,5 @@ CA	N	H1	ga_10
 CA	N	H2	ga_10
 CA	N	H3	ga_10
 [ dihedrals ]
-H1	N	CA	C	gd_14
+H1	N	CA	C	gd_19
 
diff --git a/share/top/gromos53a5.ff/aminoacids.n.tdb b/share/top/gromos53a5.ff/aminoacids.n.tdb
index 08f0beb231..af24c60609 100644
--- a/share/top/gromos53a5.ff/aminoacids.n.tdb
+++ b/share/top/gromos53a5.ff/aminoacids.n.tdb
@@ -21,7 +21,7 @@ CA	N	H1	ga_11
 CA	N	H2	ga_11
 CA	N	H3	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+H1	N	CA	C	gd_39
 
 [ NH2 ]
 [ replace ]
@@ -39,7 +39,7 @@ H1	N	H2	ga_10
 CA	N	H1	ga_11
 CA	N	H2	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+H1	N	CA	C	gd_39
 
 [ PRO-NH2+ ]
 [ replace ]
@@ -59,7 +59,7 @@ CA	N	H2	ga_11
 CD	N	H1	ga_11
 CD	N	H2	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+CD	N	CA	C	gd_39
 
 [ PRO-NH ]
 [ replace ]
@@ -72,6 +72,8 @@ N	H	gb_2
 [ angles ]
 CA	N	H	ga_11
 CD	N	H	ga_11
+[ dihedrals ]
+CD      N       CA      C       gd_39
 
 [ GLY-NH3+ ]
 [ replace ]
@@ -94,5 +96,5 @@ CA	N	H1	ga_11
 CA	N	H2	ga_11
 CA	N	H3	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+H1	N	CA	C	gd_39
 
diff --git a/share/top/gromos53a6.ff/aminoacids.n.tdb b/share/top/gromos53a6.ff/aminoacids.n.tdb
index 3d58ae40b3..6a116ec222 100644
--- a/share/top/gromos53a6.ff/aminoacids.n.tdb
+++ b/share/top/gromos53a6.ff/aminoacids.n.tdb
@@ -21,7 +21,7 @@ CA	N	H1	ga_11
 CA	N	H2	ga_11
 CA	N	H3	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+H1	N	CA	C	gd_39
 
 [ NH2 ]
 [ replace ]
@@ -40,7 +40,7 @@ H1	N	H2	ga_10
 CA	N	H1	ga_11
 CA	N	H2	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+H1	N	CA	C	gd_39
 
 [ PRO-NH2+ ]
 [ replace ]
@@ -60,7 +60,7 @@ CA	N	H2	ga_11
 CD	N	H1	ga_11
 CD	N	H2	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+CD	N	CA	C	gd_39
 
 [ PRO-NH ]
 [ replace ]
@@ -73,6 +73,8 @@ N	H	gb_2
 [ angles ]
 CA	N	H	ga_11
 CD	N	H	ga_11
+[ dihedrals ]
+CD      N       CA      C       gd_39
 
 [ GLY-NH3+ ]
 [ replace ]
@@ -95,5 +97,5 @@ CA	N	H1	ga_11
 CA	N	H2	ga_11
 CA	N	H3	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+H1	N	CA	C	gd_39
 
diff --git a/share/top/gromos54a7.ff/aminoacids.n.tdb b/share/top/gromos54a7.ff/aminoacids.n.tdb
index 119d105b8d..97d9eea4f7 100644
--- a/share/top/gromos54a7.ff/aminoacids.n.tdb
+++ b/share/top/gromos54a7.ff/aminoacids.n.tdb
@@ -21,7 +21,7 @@ CA	N	H1	ga_11
 CA	N	H2	ga_11
 CA	N	H3	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+H1	N	CA	C	gd_39
 
 [ NH2 ]
 [ replace ]
@@ -40,7 +40,7 @@ H1	N	H2	ga_10
 CA	N	H1	ga_11
 CA	N	H2	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+H1	N	CA	C	gd_39
 
 [ PRO-NH2+ ]
 [ replace ]
@@ -60,7 +60,7 @@ CA	N	H2	ga_11
 CD	N	H1	ga_11
 CD	N	H2	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+CD	N	CA	C	gd_39
 
 [ PRO-NH ]
 [ replace ]
@@ -73,6 +73,8 @@ N	H	gb_2
 [ angles ]
 CA	N	H	ga_11
 CD	N	H	ga_11
+[ dihedrals ]
+CD      N       CA      C       gd_39
 
 [ GLY-NH3+ ]
 [ replace ]
@@ -95,5 +97,5 @@ CA	N	H1	ga_11
 CA	N	H2	ga_11
 CA	N	H3	ga_11
 [ dihedrals ]
-H1	N	CA	C	gd_29
+H1	N	CA	C	gd_39
 
-- 
2.22.0