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

Justin Lemkul jalemkul at vt.edu
Wed Dec 17 03:07:44 CET 2014

On 12/16/14 9:05 PM, Justin Lemkul wrote:
> 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.

Actually, it's not a typo:

  Copy 3HTB_processed.gro to a new file to be manipulated, for instance, call it 

It's just a safety measure in case you mess something up; you haven't wrecked 
the actual pdb2gmx output.  Perhaps I should call it something different to 
avoid clashes with default names.  Apparently I had even confused myself before 
I checked...



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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