Added dummy mass for charmm TYR aromatic vsites

pdb2gmx was not able to create aromatic vsites
for charmm27 since this dummy mass center was missing.
Note that aromatic vsites are still largely untested,
and not recommended for general usage.

Fixes #587.

Change-Id: Ic7d2976536c6269d1dcf12b7d33bddab096c353f

diff --git a/share/top/charmm27.ff/atomtypes.atp b/share/top/charmm27.ff/atomtypes.atp
index 1af5eac52716fa7f424b78480cbcb7a8dda0b09b..b4d7135fcdb678707a8d1a16f08632b45b06385b 100644 (file)
--- a/share/top/charmm27.ff/atomtypes.atp
+++ b/share/top/charmm27.ff/atomtypes.atp
@@ -129,6 +129,7 @@ MNH3        0.0000 ; vsite (rigid tetrahedrical NH3 group)
 MNH2   0.0000 ; vsite
 MCH3   0.0000 ; vsite (rigid CH3 group connected to carbons)
 MCH3S  0.0000 ; vsite (rigid CH3 group connected to S)
+MW      0.0    ; Dummy mass in rigid tyrosine rings
 ; DNA and RNA section
 P       30.974 ;        Phosphorus  ### For DNA
 P2     30.974000 ;     pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str)  ### For DNA 

diff --git a/share/top/charmm27.ff/ffnonbonded.itp b/share/top/charmm27.ff/ffnonbonded.itp
index 41a6f2058c38c8d9d1c02c9e5cdb2b386aace2bf..d07e3cdf88ef4498fcd04bfa1785e4ed4556975e 100644 (file)
--- a/share/top/charmm27.ff/ffnonbonded.itp
+++ b/share/top/charmm27.ff/ffnonbonded.itp
@@ -156,6 +156,7 @@ MNH3        0       0.000000        0.00    A       0.0     0.0
 MNH2   0       0.000000        0.00    A       0.0     0.0
 MCH3   0       0.000000        0.00    A       0.0     0.0
 MCH3S  0       0.000000        0.00    A       0.0     0.0
+MW      0       0.000000        0.00    A       0.0     0.0
 ; Ions and noble gases (useful for tutorials)
 Cu2+   29      63.54600        2.00    A       2.08470e-01     4.76976e+00
 Ar     18      39.94800        0.00    A       3.41000e-01     2.74580e-02

diff --git a/share/top/charmm27.ff/gb.itp b/share/top/charmm27.ff/gb.itp
index bdd87ef10b710f6200255c012a3fb1a71d178e24..33d51c6d94169909a129d9ca24a2323e58b47285 100644 (file)
--- a/share/top/charmm27.ff/gb.itp
+++ b/share/top/charmm27.ff/gb.itp
@@ -45,3 +45,4 @@
  MNH2          0       0       0       0        0    ; dummy mass
  MCH3          0       0       0       0        0    ; dummy mass
  MCH3S         0       0       0       0        0    ; dummy mass
+ MW             0       0       0       0        0