From: Axel Kohlmeyer (
Date: Tue Jul 15 2008 - 11:20:53 CDT

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> MolAtom xxx: Exceeded maximum number of bonds (12)
SI> Can you suggest workaround for me? As i understand from log:
SI> Info) Determining bond structure from distance search ...
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

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.


SI> --
SI> Sergey Ivanov

Axel Kohlmeyer
   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.