On Mon, Oct 03, 2011, Jason Swails wrote:
> CYM is the deprotonated Cysteine. CYS is protonated. However, Francois is
> probably right in that you'll have to reparametrize the whole residue
> (charge and parameter derivation).
There is a fair amount of literature on force field simulations of P450
systems. Even if you want to slog through yet another parameterization, you
should know what has been done before. In particular, the following paper
looks very relevant:
K. Shahrokh, G. S. Yost, and T. E. Cheatham, III. "Quantum mechanically
derived AMBER-compatible heme parameters for various states of the cytochrome
P450 catalytic cycle." J. Comp. Chem. (2011) [in press].
Prof. Cheatham might be able to provide more information.
....dac
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Received on Mon Oct 03 2011 - 07:30:03 PDT
