[gmx-users] Problems with divalent cations

[Justin Lemkul]

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

-- 
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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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