[gmx-users] topolbuild and charges

Bruce D. Ray brucedray at yahoo.com
Fri Feb 3 14:23:13 CET 2012

On Friday, February 3, 2012 at 12:31 AM, Tom <dnaafm at gmail.com> wrote:

> Any one has the experience of topolbuild?
> I tried to build *top file with the software of topolbuild

>  ./topolbuild -n lipid -dir /home/computer/Tom/topbuild/topolbuild1_3/topolbuild1_3/dat/gromacs -ff oplsaa

> I chose oplssaa. But from the generated *top file,these charges in *top file can
> not match the partial charges in file (in gromacs package) of 
> /opt/gromacs-4.5.4/share/gromacs/top/oplsaa.ff/ffnonbonded.itp

> How to understand these charges on *top file, which topolbuild generates?
> Thanks for your instruction!
First, topolbuild never "generates" charges.  Unless the -charge option is specified,
the charges come from whatever is read as being the charge entry in the *.mol2 file.
If the charge type in the header of the *.mol2 file reads "INVALID", or "NO_CHARGE",
the charges are reset to 0 as the *.mol2 file is read.  If the -charge option is given,
topolbuild assigns charges given in the "Atoms data" section of the force field
parameters file in the directory pointed to by the -dir entry according to assigned
atom type.  In the case of oplsaa, the parameters file is ffoplsaa.dat, the column is
labeled charge, and the assignment is based on oplsaa atom type number.  All of
this, of course, relies on the *.mol2 file being syntactically correct according to
the rules given by Tripos, Inc.  Some programs that attempt to write *.mol2 files
fail to write complete Sybyl atom types.  Others do write complete atom types,
but sometimes have problems getting the atom type correct, most notably with
the guanidino carbon of arginine which is supposed to be C.cat

I hope this short note helps.

Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273
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