VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 31 2002 - 16:38:11 CST

Dear Lu,
  Most structures have no need for more than 8 bonds
to a single atom so this is generally a pretty rare occurence,
more likely than not, this is due to VMD's distance based bond
search finding a cluster of tightly packed atoms and is interpreting
these as bonded atoms. If you build a PSF file describing the
structure, VMD won't have to use the distance based bond search
to guess the bonds. You can use the "psfgen" package in VMD 1.7.1
or the standalone psfgen utility that ships with NAMD for this
purpose. If your PDB file contains conect records, there is a way
to process this to create a PSF file automatically let us know what
your situation is and we can provide further assistance. We intend
to rewrite the PDB loader to support conect records and secondary
structure info, but as yet have not had time to accomplish this.
Once you have a PSF file, VMD should be much happier to work with
your structure.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Mar 31, 2002 at 02:19:55PM -0500, Lu Yang wrote:
> Hello,
>
> I use VMD under linux. When I load a pdb file with 50220 atoms in it.
> It complaining "Exceeded maximum number of bonds (8)". What should I do
> to deal with this problem?
>
> Thank you very much for any suggestion.
>
> Sincerely,
> Lu Yang 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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