[gmx-users] Regarding generating topology file.

Bruce D. Ray brucedray at yahoo.com
Fri Aug 19 13:49:29 CEST 2011

On Tuesday, August 2, 2011 at 5:17 AM, Ravi Kumar Venkatraman <ravi.ipc.iisc at gmail.com> wrote:
> I have got some topology and parameter file 
for some small organic molecules from swissparam in *.mol2 format.
> I am 
trying to generate *.top, *.gro & *.itp files using topolbuild. But I
 dont know how to do. So can anybody
> give me a link or some materials 
related to this.

I'm not sure what the problem is.  The topolbuild 1.3.1 download does include documentation
on how to use it.  Is there something specific you have tried that you are having difficulties

Of course, for use with gromacs 4.5.*, one does have edit the *.top with a text editor to change
the initial include lines in the topology file to reflect the re-organization of the force field files.
Furthermore, the current topolbuild version does not support CHARMm force fields.

Also, I believe that swissparam gives those files.

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