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