[gmx-users] AMBER to GROMACS conversion

[Parker de Waal]

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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