From: Erik Lindahl Date: Wed, 11 Jun 2014 22:49:12 +0000 (+0200) Subject: Added dummy mass for charmm TYR aromatic vsites X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=b23037c805ec3e7ce35e26369a0b0b63d07e4139;p=alexxy%2Fgromacs.git 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 1af5eac527..b4d7135fcd 100644 --- 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 41a6f2058c..d07e3cdf88 100644 --- 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 bdd87ef10b..33d51c6d94 100644 --- 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