[gmx-users] Can I delete Mn^2+ ion from a protein molecule and then run MD?

[Tsjerk Wassenaar]

Hi Zhongqiao Hu,

The question is, what is the role of the Mn2+ ion? If it is involved
in the structural stability of your protein, I think you should be
well able to answer the question 'Will this lead any consequences
making the MD results unacceptable?' yourself or find yourself another
research field (just kidding). I guess that the Mn2+ ion plays a role
in keeping your protein proper. Then the following question is, why
Mn2+? Is it the native metal ion or did they use Mn2+ for
spectroscopic/electronic properties? In most cases, you can exchange
Mn2+ with Ca2+ without a problem. For Ca2+ there are parameters.
Wouldn't that do instead of Mn2+? Maybe the protein is also available
in a Ca2+ loaded form? I would suggest finding more reading regarding
your system and the variations in experiments, and also try finding
some papers regarding simulations of Mn2+ containing systems.

Hope it helps,

Tsjerk

On 11/9/06, Hu Zhongqiao <zhongqiao_hu at nus.edu.sg> wrote:
>
>
> Dear All,
> I want to do MD for a protein crystal containing Mn^2+ ion. Because gromacs
> has not provided the force field for Mn^2+ ion, I want simply delete Mn ion
> and then run MD. Will this lead any consequences making the MD results
> unacceptable?  If so, what else should I do instead?
>
>
> Zhongqiao Hu
>
> Lab E5-04-27
>
> Tel: 65161946(O)
> Department of Chemical and Biomolecular Engineering
> National University of Singapore
> 117576, Singapore
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
post-doc
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623