[gmx-users] Fwd: Fatal error: number of coordinates in coordinate file (trp-b4ion.pdb, 25093) does not match topology (trp.top, 26684)

Justin Lemkul jalemkul at vt.edu
Mon Jul 29 13:39:38 CEST 2013

On 7/29/13 6:30 AM, Jonathan Saboury wrote:
> Files: http://www.sendspace.com/file/vxcnv3
> Commands used: http://pastebin.com/raw.php?i=wPqfuUwc
> What I want to do: I just want to run the protein without the ligand in
> explicit water. Why is the coordinate file not matching topology?
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topologydoesn't
> offer much help in this case. I know the problem is the number of
> waters however.

The problem is not the waters.  Your topology specifies 3221 protein+CA atoms, 
but the coordinate file you're using only has 1630.  The problem is here:

pdb2gmx -ff amber99sb -f protein2.pdb -o trp.pdb -p trp.top -water tip3p -ignh

editconf -bt octahedron -f protein2.pdb -o trp‐b4solv.pdb -d 1.0

You're using "protein2.pdb" to move forward, after pdb2gmx acted upon it (to 
produce conf.gro) to add hydrogens.



Justin A. Lemkul, Ph.D.
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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