[gmx-users] Creating topology for Cu-containing enzyme, GROMOS96 force field.

Mark Abraham mark.j.abraham at gmail.com
Fri Aug 12 09:53:16 CEST 2016


On Wed, Aug 10, 2016 at 9:27 PM Francesca Lønstad Bleken <
FrancescaL.Bleken at sintef.no> wrote:

> I am interested in a metalloenzyme with Cu and I have found several
> studies in the literature on systems similar to mine using GROMACS and the
> Gromos force field. I see that GROMOS contains parameters for Cu, and I
> intend to keep the Cu-protein distances for the ligand atoms fixated during
> MD (as I see most of the previous papers have done). However, I do not
> understand how to prepare the topology for the cofactors with Cu, and none
> of the papers discuss this.

Note for future - if a paper doesn't provide enough details for you to
consider reproducing the work, then you should contact the corresponding
author and ask for them. Reputable people will be happy to share more
details, and often even their topology files. If you get no satisfaction,
then (eventually) the editor will retract the paper...


> pdb2gmx does not recognize it and the PRODRG server suggested in the
> excellent tutorial on protein-ligand system does not recognize Cu.
> Do you have a suggestion for how to proceed with creating the topology
> including Cu (in one case) and Cu-containing (another case) co-factors?
> Direction towards tutorials that I might have missed are also appreciated.
> Kind regards,
> Francesca
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