[gmx-users] number of coordinates in coordinate file does not match topology

Justin Lemkul jalemkul at vt.edu
Sun Jul 20 06:23:09 CEST 2014

On 7/19/14, 11:46 PM, Jonathan Saboury wrote:
> Hello,
> I am getting an error:
> "Fatal error:
> number of coordinates in coordinate file (alb-b4ion.pdb, 192933)
>               does not match topology (alb.top, 201977)"
> Number of SOL/water molecules was done automatically, so not sure why .top
> is not matching the .pdb.
> Here are the commands used: http://pastebin.com/raw.php?i=de9a8PtR
> This happens to both 1AO6 and 1BM0 on http://www.rcsb.org

The problem is here:

editconf -bt octahedron -f protein.pdb -o alb-b4solv.pdb -d 1.0

You're using the wrong coordinate file.  You should be using "alb.pdb," which is 
the output of pdb2gmx, rather than re-using the crystal structure.



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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