[gmx-users] Creating topology for Cu-containing enzyme, GROMOS96 force field.
Francesca Lønstad Bleken
FrancescaL.Bleken at sintef.no
Wed Aug 10 21:26:43 CEST 2016
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.
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