[gmx-users] Problem in running protein-ligand (Heteroatom type) system: Ligand position not in correct position

Justin Lemkul jalemkul at vt.edu
Thu Jun 19 15:07:40 CEST 2014

On 6/19/14, 5:03 AM, neeru sharma wrote:
> Dear gromacs Users,
> I am running a simulation of Protein-Ligand complex. In this case, the
> ligand consists of a GTP molecule, whose parameters I am deriving from
> PRODRG server.
> When I try to generate the complex using coordinates obtained from PRODRG
> for GTP and from pdb2gmx for Protein, the position of ligand is not the
> same.
> I am following these steps in building this protein-ligand complex.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
> I have followed the same set-up previously, for the same system and it
> worked fine then but now it is not.
> Can anyone help me out and let me know where I am wrong. Any suggestion
> would be welcome.

You're manipulating the coordinates somehow, either by allowing PRODRG to 
minimize your ligand or by altering the box dimensions of the protein (and 
thereby changing its position) before adding the ligand back in.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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