[gmx-users] DNA simulation

Justin Lemkul jalemkul at vt.edu
Tue Dec 11 14:40:28 CET 2012

On 12/11/12 5:22 AM, delara aghaie wrote:
> Dear Gromacs users
> I want to simulate dobule strand DNA using gromacs. I have read that I should use amber forcefield for DNA simulation and I have crossed a web page explaining some parameters which I should change in gromacs package to become compatible with this amber force filed.

What changes are suggested?  Note that the previous ffamber ports are no longer 
necessary, as native support for AMBER force fields has been present since 
version 4.5.

> 1) I want to know that is it possible to use straightly pdb2gmx command on pdf file of DNA (taken fron protein data bank) and choose amber forcefiled for that?


> 2) Are that changes necessary?

Probably not, but since you haven't said what those changes are, no one can give 
a definitive answer here.

> 3) If pdb2gmx does not give error how can I make sure about the correctness of procedure.

pdb2gmx will read in the parameters from whatever force field you choose.  If it 
succeeds with no errors, then all of those parameters have been applied 
successfully.  Is there some reason you believe there is a problem?



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


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