[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
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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University of Maryland, Baltimore
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Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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