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

Justin A. Lemkul jalemkul at vt.edu
Tue May 19 15:18:37 CEST 2009

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 

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.:



> I need to do some molecular minimization and dynamics including the 
> nucelic acid sequence.
> Looking for some help.
> Thank you.
> Nehme
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list