[gmx-users] AMBER to GROMACS conversion

[Parker de Waal]

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.

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