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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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