VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 15 2008 - 13:00:42 CDT

Hi,
  I agree that Axel's suggestion of generating a PSF is a generally
cleaner way of specifying bonds for use in VMD. If you feel the need
to continue using the PDB CONECT records to specify bonds (remember they
were only intended for "special" bonds, not for all bonds, which is why
VMD is also doing a distance-based bond determination), you can
workaround your present difficulties by loading the files with an extra
option:
  mol new foo.pdb autobonds off

That will prevent VMD from performing the additional distance-based
bond search in addition to reading the special bonds (in your case,
all of them) from the PDB CONECT records.

I think Axel's suggestion is the better solution, but I offer
this as a shortcut in case you're time-constrained.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 15, 2008 at 12:20:53PM -0400, Axel Kohlmeyer wrote:
> On Tue, 15 Jul 2008, Sergey Ivanov wrote:
>
> SI> Hello, developers!
>
> hi serge,
>
> SI> I want use VMD program for visualization of rahter beads on mesoscopic
> SI> level. In input for VMD i use PDB format with my own meaning of
> SI> "molecules" and "bonds". And respectivetly distance units has own
> SI> meanings.
> SI> I've tested PDB file (see attach) and found out that many bond plugged
> SI> to model from "nowhere"... Every "molecule" has not more then 3 bonds
> SI> with other ones accordingly to file but i see i quite other picture
> SI> and errors through loading:
> SI>
> SI> MolAtom xxx: Exceeded maximum number of bonds (12)
> SI>
> SI> Can you suggest workaround for me? As i understand from log:
> SI>
> SI> Info) Determining bond structure from distance search ...
> SI>
> SI> - it must be something that determines bond from exactly PDB file and
> SI> not "from distance"
>
> how do you specify bonds within a PDB file?
> which version of VMD are you using?
>
> recent versions of the PDB format reader try to read CONECT records
> and interpret them as bonds, but that requires your pdb file to
> conform to the PDB standard.
>
> the simpler way to specify bonds explicitly (and cleaner in my opinion)
> is to write a .psf format file. the NAMD tutorials have some explanation
> of the PSF format. you don't have to generate a complete .psf file. for
> visualization purposes only the atoms and bonds info are needed (and
> used).
>
> with the very latest VMD you should also be able to tell VMD to not
> try to guess bonds when loading from the command line prompt.
> please check the documentation.
>
> cheers,
> axel.
>
> SI>
> SI> --
> SI> Sergey Ivanov
> SI>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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