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

Marlon Sidore marlon.sidore at gmail.com
Thu Aug 11 10:23:48 CEST 2016


pdb2gmx needs the parameters for your co-factors, else it won't recognize
it. It should recognize the Cu alone though, if it has the same name as in
the topology.
You will probably need to obtain the parameters for your co-factors from
the relevant papers. If you can get ready-to-use files, cool, but you might
need to build them yourself from the parameter tables found in the papers.

The parameters are usually 2 or 3 files (+1 if it is covalently bound to
your protein):
- One .rtp, with the molecule definition, atom numbering, charges and
- One or two .itp, for the bonded (bond, angle and dihedral constants) and
the non-bonded parameters (if you have to define atom types)
- A specbond.dat file if your co-factor is covalently bound to your
protein, to create these bonds. You'll also need special amino-acids in
your .rtp file with one hydrogen less for example.

Hope that helps.

Marlon Sidore

PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille

2016-08-10 21:26 GMT+02:00 Francesca Lønstad Bleken <
FrancescaL.Bleken at sintef.no>:

> 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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