[gmx-users] dna-drug simulations

Justin Lemkul jalemkul at vt.edu
Sat Jan 26 14:13:02 CET 2013

On 1/26/13 4:18 AM, amna khan wrote:
> hi, all ,
> i want to simulate dna with ligand/drug
> i am getting error in generating he topology for dna .

We can't help you unless you show us what the error is and provide (at the very 
least) your exact pdb2gmx command.

> I'm unable to do using the  pdb2gmx with any of the force fields. Could
> anyone please tell if I can get any tutorial for the DNA-drug simulation.

Exercise Google here.  If it exists, you should be able to find it by searching 
or visiting gromacs.org.

> or which forcefield should i use ?

What does your analysis of the literature suggest would be the best choice?



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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