I am doing a molecular modeling of metal binding of arsenic with protein. My lecturer said that arsenic model is not in database. I have to create an arsenic model before i can parameterized it. how to model an arsenic? what software that i have to use?
You can take the simplest model from the universal force fields, such as UFF or ad hoc model of Abalone.
To create more accurate models OPLS approach can be used, that is to take a few low polar liquids containing arsenic and choose the parameters of the Lennard-Jones so that the density and the heat of vaporization of liquids were consistent with experiment.
Abalone at http://www.biomolecular-modeling.com/Abalone/index.html
UFF has implemented for example in ArgusLab http://www.arguslab.com/
You can use the following tool. It covers 80 different metals and As is one of them.
http://ambermd.org/tutorials/advanced/tutorial20/mcpb.htm
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674
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