From: Axel Kohlmeyer (
Date: Thu May 29 2008 - 13:54:24 CDT

On Thu, 29 May 2008, Demian Riccardi wrote:

DR> Hello,


DR> I'm trying to an visualize elastic network model of a protein where the
DR> bonds are long and the number of bonds/per atom exceeds physical norms. I
DR> generate a psf which has 758 bonds, but when I read it in only 268 register
DR> with VMD. Does VMD purge excessive bonds or does it just complain (as
DR> written below) and do what it's asked to do? If it's the latter, then

the maximum number of bonds per atom is a compile time option
and limited by default to 12 for memory and efficiency reasons.

you have to recompile VMD from source to change this.


DR> there's possible something wrong with my psf.
DR> Demian
DR> error message:
DR> ERROR) MolAtom 24: Exceeded maximum number of bonds (12).
DR> ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps atom
DR> ERROR) BaseMolecule: coordinates are in the wrong units?
DR> ERROR) BaseMolecule: Silencing bonding error messages.

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.