I want to run protein-Ligand simulation where gold atoms are ligand. Gromacs is showing error for that. I tried to use Prodrug server also, but it is not generating coordinates for gold atoms.
Can anyone help me in this?
It is difficult to find force field for the gold atom compatible with biomolecular force field. Depending on what you are trying to do, you may consider to use hybrid QM/MM scheme, where binding site and gold atom are treated at the quantum level, and the rest of the peptide and water at the classical level.
There just a few force fields that include gold element. It's for sure implemented in UFF, I've seen some papers on Au-S-C parametrization in ReaxFF and that's about it. The quickest (in the sense of amount of work put into it) method would be, as Alexey suggested, to use QM/MM with Au atom and all nearest neighbors describe by QM (modern DFT should do fine) and the rest by standard force field.
hi you can use GOLP force filed in gromacx software. this ff is compatible for gold and protein interaction.
Dear Chetan,
I share you the forfield parameters to simulate Gold nanoparticle in gromacs, it seems the link is not already available. I also have the force field for CHARMM if you want it.
references:
Hi Bello,
I would like to simulate the gold nano particle with the golp-charmm parameters. How to generate the virtual atom positions for the gold nanoparticle with (1 1 1) facet structure?
Dear Muthusivarajan
I share you the forcefield parameters for Gold-charmm.
Greetings,
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