[gmx-users] tyrosyl radical force field
jalemkul at vt.edu
Wed Oct 3 13:12:47 CEST 2012
On 10/3/12 6:00 AM, tarak karmakar wrote:
> Dear All,
> Is it possible to deal a protein with tyrosyl radical in Molecular
> Dynamics Simulation ?? If possible can you please provide me the
> reference or literature where I can find the force field parameters
> for tyrosyl radical ?
Molecular mechanics force fields do not deal explicitly with electrons, so don't
expect anything particularly interesting to happen with a so-called radical
tyrosine unless you're using QM methods. You could perhaps parameterize a
deprotonated tyrosine residue that, as input to QM software, has the number of
electrons in the radical species. You may then have to come up with new atom
types depending upon whether or not the LJ parameters (especially for the
phenolic O) are satisfactory.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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