[gmx-users] fatal erroe in prorein-ligand comlex

Justin Lemkul jalemkul at vt.edu
Wed Dec 17 13:55:50 CET 2014

On 12/17/14 12:50 AM, Abid Channa wrote:
> hi gromacs users
> i got error in step four in protein-ligand complex how can i fix it:
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 36526)
>              does not match topology (topol.top, 365267)
> when i want to ran this:
> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
> i add my ligand drg.gro in protein_processed.gro.
> Thanks,,

Somehow your topology specifies 10x the number of atoms of the coordinate file, 
indicating some severe duplication error.



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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