Re: Bad global bond count! (48842 vs 48843)

From: Ashutosh Shandilya (
Date: Tue Apr 10 2018 - 11:41:32 CDT

Extrabond file for nucleic acid is generated using VMD. I could see the
numbering index in extrabond is somewhat different than nucleic acid
numbering. I generated nucleic acid with the same selection using VMD it
generates only nucleic acid. Could not attache psf file associated to pdb
file as it exceeds the size limit for namd user mailing list. If any one
could provide any insight that would help.

Many thanks,

On Tue, Apr 10, 2018 at 10:47 AM, Ashutosh Shandilya <>

> Dear NAMD Users
> I am trying to run targeted MD with extra bond restraints. I am getting
> this error, I checked for possible solutions online to check for duplicate
> atoms but could not find any. Even during visualization there are no
> unusual bonds. I ran step wise minimization and equilibration with
> restraints and constraints which ran fine. Also tried increasing cut off
> with no effect.
> Attached are my extra bond file (only nucleic acid) and pdb and input
> file. Kindly suggest.
> Many thanks,
> Ash

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