VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 23 2002 - 22:10:19 CDT

Dear Marcela,
  The easiest way is to provide VMD with a structure file that includes
bonding information, such as a PSF file etc.
VMD doesn't yet know how to process PDB conect records itself,
but Andrew Dalke wrote a script that will create a PSF from a PDB with
conect records, its in the TB web site in the "MDTools" area if I recall
correctly),
If you are just giving VMD a PDB file it calculates bonds based
on a distance search, which is probably the
reason you're not seeing a bond on the atom that you are expecting to.
If you need more help with this, send another note to vmd_at_ks.uiuc.edu,
I'm out of town at a conference (siggraph) so I'm unable to do much more
than basic and infrequent email replies until next week.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jul 20, 2002 at 04:20:08PM -0400, Marcela Madrid wrote:
> Is there a way to tell VMD to draw bonds ? I have a Pt atom that is
> suppose to be
> bonded but VMD does not draw the bonds. thanks, Marcela
> Can you please reply to mmadrid_at_psc.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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