[gmx-users] AMBER to GROMACS conversion

Mark Abraham mark.j.abraham at gmail.com
Wed Jun 26 01:57:45 CEST 2013

On Wed, Jun 26, 2013 at 1:16 AM, Parker de Waal
<Parker.deWaal09 at kzoo.edu> wrote:
> Hi Everyone,
> I'm very interested in using a set of recently derived AMBER heme
> topologies within GROMACS to perform MD simulation on P450 enzymes.
> Specifically I would like to use parameters found here
> https://gist.github.com/anonymous/995efe4d44c6cf0584ef
> After trying to use topolbuild1.3, found on the GROMACS website I was
> unable to successfully make the installation (using Ubuntu 12.04). While no
> errors occurred during the make process trying to use topolbuild results in
> 'topolbuild: command not found' within the same folder as the previously
> built file.

I have nothing to say on point, but the error message is normal when
you do not have the current working directory in your path. Try


> If anyone has any insight into how to convert these AMBER topologies into
> GROMACS compatible .itp .gro files I would be extremely grateful.
> Best,
> Parker
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