[gmx-users] AMBER to GROMACS conversion

Parker de Waal Parker.deWaal09 at kzoo.edu
Wed Jun 26 02:10:51 CEST 2013


Hi Mark,

That was silly mistake on my part... thank you for pointing that out.

Now I've been able to successfully convert the two .mol2 files into gromacs
.itp however I am unsure how to convert the .frcmod file as well.

Cheers,
Parker


On Tue, Jun 25, 2013 at 7:57 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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
> ./topolbuild
>
> Mark
>
> > 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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