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

João M. Damas jmdamas at itqb.unl.pt
Thu Aug 11 16:41:04 CEST 2016

Hi Francesca,

For previous works on copper proteins (
http://pubs.acs.org/doi/abs/10.1021/ct500196e), I have used specbond.dat as
Marlon suggested for coppers bound to the protein. For coppers bound to a
co-factor, I would assume you are building an .itp for the co-factor, so I
would include them directly on that .itp file.


On Wed, Aug 10, 2016 at 8:26 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. 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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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

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