[gmx-users] Regarding atom numbering in .top and .gro files

Justin Lemkul jalemkul at vt.edu
Sat Sep 28 17:29:33 CEST 2013

On 9/28/13 11:20 AM, bipin singh wrote:
> Hi all,
> I want to put off constraint between some bonds in my system based on their
> atom numbers but the .gro file and .top file atom numbers do not match,
> because I used .pdb file to generate this .top file using pdb2gmx. (the top
> files contains the atom numbers based on this initial input .pdb file and
> the subsequent .gro file contains different atom numbering)
> I know that grompp generate constraints based on atomtypes in .top file but
> If I use the .pdb file (used during pdb2gmx) to do this will it be  fine,
> as I will be using this .top file with .gro file for grompp.

As with all bonded interactions, the numbers in the coordinate file are 
irrelevant.  You can only specify bonded interactions based on the atom numbers 
in the [moleculetype] in the .top file.



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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