[gmx-users] grompp

Justin Lemkul jalemkul at vt.edu
Wed Jun 18 13:53:01 CEST 2014

On 6/18/14, 3:02 AM, Meenakshi Rajput wrote:
> Hi gromacs users
> I run the grompp command
> (grompp_d -v -f minim.mdp -c sol.gro -o min.tpr -p hsa.top)
>   to generate .tpr file but i got the following error
> Fatal error:
> number of coordinates in coordinate file (sol.gro, 140012)
>               does not match topology (hsa.top, 140027)
> When I opened gro file, only protein and sol molecules are seen in .gro
> file but no ligand molecules. I dont know why it is happening..
> Can anybody help me?

Not really.  You haven't said how you've been keeping track of the system's 
contents or how you've constructed the coordinate file.  You're missing 15 atoms 
somewhere - does that correspond to the ligand?  Did you modify the coordinate 
file in some way?



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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