VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu May 29 2008 - 13:54:24 CDT

On Thu, 29 May 2008, Demian Riccardi wrote:

DR> Hello,

demian,

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.

cheers,
   axel.

DR> there's possible something wrong with my psf.
DR>
DR> Demian
DR>
DR>
DR> error message:
DR>
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.
DR> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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