[gmx-users] Can I delete Mn^2+ ion from a protein molecule and then run MD?
tsjerkw at gmail.com
Thu Nov 9 09:32:06 CET 2006
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,
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
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read
Tsjerk A. Wassenaar, Ph.D.
NMR, Utrecht University,
3584 CH Utrecht, the Netherlands
More information about the gromacs.org_gmx-users