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

[Justin A. Lemkul]

Nehme El Hachem 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)?

The first step is probably to search in the literature for anything similar. 
Has anyone attempted such work?  Is there precedent for making the force field 
choice?

The only force field I know of that contains deprotonated cysteine that has also 
been implemented in Gromacs is AMBER (residue "CYM").  The ffamber ports are 
available for download online.

Another thing to consider is whether any MM force field will adequately describe 
your coordination complex, i.e.:

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

-Justin

> 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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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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