[gmx-users] metal ion go out of protein after md

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 11 10:26:04 CET 2009

Nothing, except reading more about periodic boundary conditions. It
doesn't hurt though to understand that binding of ions such as Mn to
proteins involves charge transfer effects, that are hard to model
properly. This will cause a (further) deviation between your results
and reality. So be careful in drawing conclusions.



On Wed, Mar 11, 2009 at 8:41 AM, Homa Azizian <hazizian at razi.tums.ac.ir> wrote:
> Hi
> MN in my active site participate in electrostatic intraction. I did not
> define any covalant bonds in topology file.
> What should I do in the case of Electrostatic intraction?
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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