From: John Stone (
Date: Tue Oct 19 2010 - 10:45:43 CDT

  In abscence of a structure file that explicitly specifies bond information,
VMD uses a distance-based bond determination heuristic. If you are seeing
a bond where there should not be one, or you are expecting to see one but
there isn't one, then you should try to create a PSF file or another
structure file type that explicitly specifies the bonds for your structure
so that VMD doesn't have to guess.

  John Stone

On Tue, Oct 19, 2010 at 11:36:43PM +0800, Joyce Tan wrote:
> Hi.
> I have my 5000 frames .xtc and .gro loaded into vmd.
> And I was trying to convert one of the frames into pdb through this:
> set A [atomselect top protein frame 4998]
> $A writepdb xx.pdb
> When I load xx.pdb into the vmd, one atom from one residue is connected to
> another atom from another residue. This particular bonding was not found
> in the trajectory file. I really don't understand why is this happening.
> Can someone help?
> Thanks.
> Regards,
> Joyce

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078