[gmx-users] Help on itp and pdb

Justin Lemkul jalemkul at vt.edu
Fri Sep 6 23:29:40 CEST 2013

Please don't reply to the entire digest; the archive is hopelessly confused as 
it is, but let's not make it any worse ;)

On 9/6/13 2:29 PM, R R S Pissurlenkar wrote:
> If I use the topology and coordinates of a small molecule from ATB for docking
> (structure.pdb / structure.itp which match in atom numbering and sequence);
> after docking and saving the structure_dock.pdb, the atom numbering does not
> match the numbering in the structure.itp file.  This causes errors during
> simulation.
> How to regular the numbering so that it matches the structure.itp file from ATB

The numbering of the atoms in the coordinate file should have no relevance on 
the .itp file, which must be numbered from 1.  If atoms in the coordinate file 
are out of order with respect to the topology, there's no real choice but to 
reorder them manually in a text editor, but that's only something you should 
ever have to do once.

If you need more explicit advice, please provide exact input, output, and any 
relevant error messages (copied and pasted from the terminal, please).



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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