[gmx-users] gromacs

[Justin Lemkul]

On 7/31/14, 1:16 AM, Meenakshi Rajput wrote:
> hi gromacs users
> I have done the whole mdrun simulation of my protein human serum albumin
> complex with ligand and i got all the files. But when i opened the pdb file
> obtained after md simulation in pymol to see the interaction, ligand went
> to some other place. It was not in the active site. please tell me what is
> the problem, where i m wrong?
>

Most likely a periodicity effect.  Re-image with trjconv.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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