[gmx-users] MD with DNA double strand

Justin Lemkul jalemkul at vt.edu
Thu Sep 17 15:29:04 CEST 2015

On 9/17/15 2:03 AM, Amali Guruge wrote:
> Dear Gromacs users,
> I want to do a molecular dynamic simulation for my enzyme-ligand complex.
> The enzyme is topoisomerase I. I used the pdb id 1K4T for the simulation
> and I need to keep the DNA double strand with the enzyme.
> I replaced the 5'-sulfhydryl group into a 5'-hydroxyl group before starting
> the simulation.
> I gave the command 'pdb2gmx -f receptor.pdb -inter -p system.top -o
> recep01.pdb -ignh'. I selected AMBER99 as the force field while SPC/E was
> used as the water model.
> Then I got the following error.
> Fatal error:
> Atom O in residue DG 11 was not found in rtp entry DG with 33 atoms
> while sorting atoms.
> How can I solve this problem? Can anyone help me?

You need to make sure the protein and each DNA strand are in separate chains, 
then interactively select appropriate termini with pdb2gmx -ter.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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