VMD-L Mailing List

From: Demian Riccardi (riccardi_at_chem.wisc.edu)
Date: Thu May 29 2008 - 13:18:09 CDT

Hello,

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

Demian

error message:

ERROR) MolAtom 24: Exceeded maximum number of bonds (12).
ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps
atom coordinates are in the wrong units?
ERROR) BaseMolecule: Silencing bonding error messages.