On 10/3/12 7:49 AM, tarak karmakar wrote:
Thanks Justin,
Actually if I would remove the proton from the tyrosine -OH and add
the corresponding charge of the Hydrogen to the phenolic oxygen to
keep the residue neutral then wouldn't it be convenient to think as if
it's a radical ?
That doesn't sound legitimate to me at all. A radical species is electronically
very different.
-Justin
On Wed, Oct 3, 2012 at 4:42 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
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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