xianqiang wrote:
You do not need to fix the copper in the calculation. There are must be
some negative charged residues around the copper. Therefore, the copper
will located at the place where it should be.
I agree that a position restraint on copper is not appropriate, but I strongly
disagree with the assumption that it will simply be held in place by virtue of
negative charges. I know of many cases where the MM approximations and
electrostatic interactions were insufficient to preserve active-site geometry.
There are a number of QM/MM studies that have concluded that fixed point charges
on such species suffer from many limitations, not the least of which are
inductive effects and the inability to account for orbital geometry. A series
of distance restraints between ligating residues and the copper ion itself may
be the best approach for "standard" MD simulations.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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