On 2/28/13 2:28 PM, Thomas Schlesier wrote:
Dear all,
first i apologise for the not completely to GROMACS related question.
I have heard that the description of divalent cations in classical MD
simulations is sometimes flawed. Cations leaving the binding side of proteins...
The GROMACS online documentation (under 'exotic species') mentions quantum
effects, but gives no reference :(
Well, the wiki isn't peer reviewed, so we don't have to cite our sources ;)
The only reference you really need is any basic general chemistry textbook.
Coordination geometry is the most intuitive item missing from MD force fields.
The fixed charge approximation is a poor one in the context of metal ions, since
they delocalize charges very strongly across anything ligated to them.
Does anybody know a publication, which discusses the topic (problems of divalent
cations)?
Here's one: dx.doi.org/10.1002/jcc.20876
Just about any QM/MM study of enzymes with cations in the active site will
describe some problems with fixed charges. There is one study on carbonic
anhydrase from Kenneth Merz's lab that I can recall, though I don't have a DOI
link for it. Probably sometime in the late 90's, 1996 or 1997.
-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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