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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--
========================================
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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