[gmx-users] copper and His residues

[Justin A. Lemkul]

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

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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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