[gmx-users] ATB

Justin Lemkul jalemkul at vt.edu
Wed Apr 1 22:35:39 CEST 2015

On 4/1/15 8:30 AM, Vasiliy Znamenskiy wrote:
> Dear All
> Does the type of chemical bond (single, double, triple), built by JSME
> Molecular Editor, directly influence on the final results of Automated
> Topology Builder (http://compbio.biosci.uq.edu.au/atb/ ), not by number of
> built protons?
> I built a molecule with a some double bond, number of protons is correct,
> however finally ATB's "Show structure" option shows this bond as a single
> bond, however number of protons there as for a double bond.
> Is it an error of visualization only or built topology files have errors?

The topology is definitive, not whatever is rendered.  That goes for all 
software.  Most aren't intelligent enough to represent bond order correctly.



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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