[gmx-users] copper and His residues

xianqiang xianqiangsun at 126.com
Wed Jan 4 09:59:36 CET 2012


Xianqiang Sun

Email: xianqiang at theochem.kth.se
Division of Theoretical Chemistry and Biology
School of Biotechnology 
Royal Institute of Technology
S-106 91 Stockholm, Sweden  

At 2012-01-04 04:04:46,"Justin A. Lemkul" <jalemkul at vt.edu> wrote:
>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 A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080

I agree your opinion on some degree. But I think he should do the simulation with the copper at reasonable place  without restraint at first. If it is not work, the electrostatic interaction may be not  strong enough for locating the copper. Then, he can redo the calculation with distance restraint between the  copper and residues nearby. So the choice should depend on the system he worked on.
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