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
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==
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