[gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

[Tsjerk Wassenaar]

Hi,

Have a look at

http://wiki.gromacs.org/index.php/Parameterization
and
http://wiki.gromacs.org/index.php/Exotic_Species

Next to that, also consider that you are talking about a site with -2
formal charge (ZnS4)2-. How likely is that? From QM studies, it seems
much more likely that there are 1 or 2 protons associated with the
cluster. If you manage to model that properly, let me know; I'd be
interested in that.

Cheers,

Tsjerk

On Tue, May 19, 2009 at 2:01 PM, Nehme El Hachem <ne21 at aub.edu.lb> wrote:
> Hello,
>
> I have a DNA-Zinc finger complex. What are the suitable forcefields for that
> type of complexes (the zinc ion is coordinated to 4 deprotonated cysteines)?
> I need to do some molecular minimization and dynamics including the nucelic
> acid sequence.
> Looking for some help.
>
> Thank you.
>
> Nehme
>
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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
F: +31-30-2537623