From: Sergey Ivanov (
Date: Thu Jul 17 2008 - 08:14:39 CDT

It's that exactly what i want if it would work... With PSF i would
deal in future but now have a series of troubles:
1) These options work only in vmd interpreter and they are not a
command line options. But it wold be great to change \shell\command
subkey in windows registry for vmd.exe (i have windows client as you

2) After generatinng by this script it shows:
 Info) Analyzing structure ...
Info) Atoms: 1208
Info) Bonds: 12 (!!!!!!!!!!!!!!!!!!!!11- i know exactly what bonds
it found but why???)
Info) Residues: 1201
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1201 Protein: 0 Nucleic: 0
My PDB-file consists only of HETATM and CONECT sections. I would
attach it but your mail-server don't support it as i understand.

2008/7/15 John Stone <>:
> 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
> 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
>> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: Phone: 217-244-3349
> WWW: Fax: 217-244-6078

Sergey Ivanov