Make sure masses are copied from termini databases

Masses should always be copied from termini databases,
where they are mandatory since they are specified before
the charge, rather than picking them from atomtypes.atp.
This patch also adjusts a few of the default CHARMM27
charges in atomtypes.atp that deviated in the 3rd decimal.

Fixes #1207.

Change-Id: I6f0c87989ae285ff435cd56c64432988c6634824

diff --git a/share/top/charmm27.ff/aminoacids.n.tdb b/share/top/charmm27.ff/aminoacids.n.tdb
index 53fc89d5034a747aec39c5e01d28bb69f5841a8e..87d81835ac0eb11d262358ba0ba22fcbffd2dd54 100644 (file)
--- a/share/top/charmm27.ff/aminoacids.n.tdb
+++ b/share/top/charmm27.ff/aminoacids.n.tdb
@@ -2,7 +2,7 @@
 
 [ GLY-NH3+ ]
 [ replace ]
- N     N       NH3             14.0027 -0.3
+ N     N       NH3             14.007  -0.3
  CA    CA      CT2             12.011  0.13
 [ Add ]
  3     4       H       N       CA      C
@@ -12,7 +12,7 @@
 
 [ NH3+ ]
 [ replace ]
- N       N     NH3             14.0027 -0.3
+ N       N     NH3             14.007  -0.3
  CA      CA    CT1             12.011  0.21
  HA      HA    HB              1.008    0.10
 [ Add ]
@@ -23,7 +23,7 @@
 
 [ PRO-NH2+ ]
 [ replace ]
- N       N     NP       14.0027 -0.07
+ N       N     NP       14.007 -0.07
  CA      CA    CP1      12.011  0.16
  CD      CD    CP3      12.011  0.16
 [ add ]
@@ -33,7 +33,7 @@
 ; 
 [ NH2 ]
 [ replace ]
- N             NH2             14.0067 -0.96
+ N             NH2             14.007 -0.96
  CA            CT1             12.011  0.19
  HA            HB              1.008   0.09
 [ add ]
@@ -46,7 +46,7 @@
 ; 
 [ GLY-NH2 ]
 [ replace ]
- N             NH2             14.0067 -0.96
+ N             NH2             14.007 -0.96
  CA            CT2             12.011  0.10
 [ add ]
  2     4       HT      N       CA      C
@@ -58,7 +58,7 @@
 ; 
 [ PRO-NH ]
 [ replace ]
- N             NP      14.0027 -0.40
+ N             NP      14.007  -0.40
  CA            CP1     12.011  -0.08
  CD            CP3     12.011  -0.10
 [ add ]

diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp
index 2110a4b32e5d7747649855e736db2a58223ebff3..befb6a6a7ff01f3a912d874a5893680b7dbbf242 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@ -442,7 +442,7 @@ void choose_watermodel(const char *wmsel, const char *ffdir,
     sfree(model);
 }
 
-static int name2type(t_atoms *at, int **cgnr, gpp_atomtype_t atype,
+static int name2type(t_atoms *at, int **cgnr,
                      t_restp restp[], gmx_residuetype_t rt)
 {
     int         i, j, prevresind, resind, i0, prevcg, cg, curcg;
@@ -492,9 +492,8 @@ static int name2type(t_atoms *at, int **cgnr, gpp_atomtype_t atype,
             j                = search_jtype(&restp[resind], name, bNterm);
             at->atom[i].type = restp[resind].atom[j].type;
             at->atom[i].q    = restp[resind].atom[j].q;
-            at->atom[i].m    = get_atomtype_massA(restp[resind].atom[j].type,
-                                                  atype);
-            cg = restp[resind].cgnr[j];
+            at->atom[i].m    = restp[resind].atom[j].m;
+            cg               = restp[resind].cgnr[j];
             /* A charge group number -1 signals a separate charge group
              * for this atom.
              */
@@ -1562,7 +1561,7 @@ void pdb2top(FILE *top_file, char *posre_fn, char *molname,
                atoms, nssbonds, ssbonds,
                bAllowMissing);
 
-    nmissat = name2type(atoms, &cgnr, atype, restp, rt);
+    nmissat = name2type(atoms, &cgnr, restp, rt);
     if (nmissat)
     {
         if (bAllowMissing)