Dear All,
I am trying to simulate Fe hydrogenases. however, I am unable to parametrise the FeS clusters. There are 4 different types : Fe3S4, Fe4S3, Fe4S4 and Fe attached to Carbon and Nitrogen.
I have come across some papers on simulation of the hydrogenases on NAMD. We dont have NAMD in the lab. We have gromacs and amber. on gromacs, the errors are covalent residues and for amber , i need the parameter files of clusters.
Can anyone explain on how to go about doing this simulation?
I remain grateful
Thank you
Ayesha Fatima
Using the amber force field try MCPB.py code.
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
In principal If you want to obtain bond and angle potentials' force-constants you can do it with Seminario Method: https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-461X(1996)60:7%3C1271::AID-QUA8%3E3.0.CO;2-W . You just need the Hessian which can be obtained with ORCA or other quantum-chemistry software. there are already many programs that do this like MCPB.py or Hess2FF.
Dear Aashish and Dmitry
Thank you for your answers.
I started the simulation on Desmond@Schrodinger. I did not have to prepare anything as in parameters. Schrodinger could do it. However, it has only 1forcefield choice and that is OPLS4.
Thank you once again.
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