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

Justin Lemkul jalemkul at vt.edu
Wed Dec 17 03:05:50 CET 2014

On 12/16/14 5:22 PM, Yaser Hosseini 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, 144131)
>               does not match topology (topol.top, 144171)
> 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.
> beside i cant find conf.gro that you say in this toturial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/02_topology.html

conf.gro is the default output name from pdb2gmx; it's just a typo in the tutorial.

The solution to your problem is always the same - proper bookkeeping.  Your 
topology specifies something that is not in the coordinate file (the ligand, 
perhaps?) that has 40 atoms.



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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