[gmx-users] MD run complete but ligand not showing up

Justin Lemkul jalemkul at vt.edu
Mon Aug 3 03:00:45 CEST 2015

On 8/2/15 6:06 AM, su wrote:
> Hello I am confused about my MD results.According to Justin's tutorial of
> protein-ligand MD, i performed short 1ns md on my protein-ligand system.
> After completion, when i opened up the md.gro and md.xtc in VMD, it is only
> showing up protein.Ligand is absent from box. Also, no .trr file is

Molecules can't disappear.  Either you never added the ligand or your attempts 
to visualize it are using the wrong residue name.  Open the coordinate file in a 
text editor; if the ligand isn't there then it never was.

> generated. When i tried to view hydrogen bond interactions, it gave fatal
> error that no topol.trr is found. I have also prepared movie.pdb and viewed

You won't get a .trr unless you ask for one by setting nst[xvf]out > 0.

> it in pymol, but in that also ligand is not showing. Can anyone please tell
> me if this is a common error? do i need to insert the ligand gile manually? I

If you followed my tutorial, you should know the answer to that already :)

> can attach the files if required. Regards Suniba

The mailing list does not accept attachments, but in this case no additional 
files are needed.



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


More information about the gromacs.org_gmx-users mailing list