[gmx-users] Unusual bond

Justin Lemkul jalemkul at vt.edu
Wed May 25 13:03:33 CEST 2016

On 5/25/16 6:47 AM, Alexander Alexander wrote:
> Dear Gromacs user,
> The VMD report below warning when I load my minimized ".gro" structure;
> Warning) Unusual bond between residues:  13724 (none) and 22887 (waters).
> The VMD does not report any warning when I load my structure "gro" file
> before energy minimization, but when I minimized it in orde via "steep and
> cg" integrator, this shows up for the final structure while the force has
> already met the criteria and potential also nicely shows a negative
> convergence.
> I was wondering if this warning has something to be worried about?

VMD guesses where bonds should be based on distance.  It often gets them wrong. 
The topology is definitive; VMD is not.



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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