VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 10:45:43 CDT

Hi,
  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.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

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: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078