[gmx-users] bond, angles and dihedrals in the topology file

Justin Lemkul jalemkul at vt.edu
Wed Sep 30 13:33:31 CEST 2015

On 9/30/15 7:21 AM, faride badalkhani wrote:
> Dear all,
> Could you tell me what is wrong when there are some strange bond, angles
> and dihedrals in the topology file after executing pdb2gmx command?
> for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
> generate them as [bonds]. A similar problem occurs in case of angles and
> dihedrals.

Impossible to say without knowing what you're actually doing.  Please always 
provide a full description of your system, your pdb2gmx command, and any 
relevant output, snippets of files, etc.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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