[gmx-users] Help on itp and pdb
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
> 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.
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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