I am working with an enzyme which has Zinc in its catalytic site.
I want to further continue my study using molecular dynamics simulation, as the zinc is involved in the catalysis process. I tried the simulation with dummy atoms approach but the mass gets distributed between dummy atom (DZ) and zinc, and has an effect on catalysis.
So if anyone has any idea about zinc parameter please let me know.
There are parameters for Zn in the CHARMM, AMBER, and GROMOS force fields. There is no zinc in the OPLS force field files that come with GROMACS, so I don't know about it. If you are really interested in the reaction, you will have to do QM/MM and will then not need the parameters since the zinc will be in the QM region.
You can take a look at J. Chem. Theory Comput., 2013, 9 (6), pp 2733. They have three separate sets of parameter for various divalent ions (which includes zinc) in spce, tip3p and tip4pew water models.
gave you tried http://davapc1.bioch.dundee.ac.uk/prodrg/
I think you may get what you require
I am a student only (final year MS, did some similar stuff long back)
There are parameters for Zn in the CHARMM, AMBER, and GROMOS force fields. There is no zinc in the OPLS force field files that come with GROMACS, so I don't know about it. If you are really interested in the reaction, you will have to do QM/MM and will then not need the parameters since the zinc will be in the QM region.
@ Brian Novak Thank you very much
You are absolutly right.
Currently I am doing the same focusing on QM/MM studies. Zinc along with active site residues treated in QM region and remaining in MM region.
As an alternative, you may do your own parametrization with the code GULP for a large variety of force fields. The code is free and can be download from http://projects.ivec.org/gulp/ after a registration.
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