[gmx-users] TOPOLBUILD

Ray, Bruce D bray at iupui.edu
Sat Apr 8 14:17:06 CEST 2017

On Apr 8, 2017, at 13:34:08 +0530 Vidya Devi <vidyadevi2811 at gmail.com> wrote:

> Hi gromacs users,
> I am using topolbuild to generate oplsaa force field parameters.
> ./topolbuild -n LIGAND.mol2 -dir
> C:/cygwin64/usr/local/gromacs/share/gromacs/top/oplsaa.ff -meas
> Need correct parameters
>                        .
> What should I do to get correct parameters?
> Thanks,
> Vidya.R

The correct parameters are included with the topolbuild files.
In the topolbuild package, there is a directory called dat
Whereever you placed that directory is where the -dir parameter
should be pointed.  Ordinarily, one would run topolbuild in the
directory of the mol2 file from which the topology is to be built.
This ensures that the topology is built in the same directory as
the mol2 file and _not_ in the directory of the topolbuild binary.
Thus, for oplsaa, one would write a command that has a general form:
   /path_to_topolbuild/topolbuild -n LIGAND -dir /path_to_topolbuild_data/dat/gromacs -ff oplsaa
Note that the directory pointed to is a topolbuild directory and not
part of the gromacs distribution, and not to a specific forcefield
file.  This is because automatic topology generation needs more atom
typing information.

Examples of commands are given in the file PROGRAM_TESTING DONE.txt
General explanation of program commands is given in the file README.txt
Warnings about the limitations of automatic topology generation are
given in the file limitations.txt

Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202

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