From: John Stone (
Date: Tue Apr 05 2005 - 17:41:22 CDT

  I just tried out your "BigConfig.pdb" structure and I too encountered
the behavior you've described. This is certainly a bug in the way VMD
handles your structure, it is not size-related as far as I can tell.
The "too many bonds" warning indicates that the automatic bond search
is finding a LOT of atoms spaced so closely together that they are
considered bonded, the warning indicates that it has gone far past
the point of any realistic biological structure, particularly since
I get screenfulls of these warnings. I'm going to have to dig a bit
deeper to determine what's going on here, as the program is exiting
abnormally which is should not be doing in any case. I'll let you guys
know when I find out what's happening with this particular structure.

  John Stone

On Mon, Apr 04, 2005 at 12:31:31PM +0200, Nicolas CHARVIN wrote:
> >To load it, get the files in that directory, then execute VMD with:
> > vmd -e virus-simple.vmd
> >
> >Does VMD successfully render the structure on your machine?
> yes, it loads very smoothly. I get 2.8 fps in VDW mode, and 62 fps
> (maximum) in lines mode.
> By the way, the "Determining bond structure from distance search" seems to
> perform very quickly for a 395250 atoms molecule.
> When I try to load my "test" big molecule ( 640,000 atoms, grab it at
> , I get a "MolAtom #### : Exceeded maximum number of bonds (8)" error
> during "Determining bond structure from distance search" phase, and it
> seems to loop forever on Molatom number, which is new (vmd 1.8.2 crashed).
> By the way, Qmol can read and render it fairly smoothly.
> I do not know much about this big molecule, and about bonds and structure,
> stuff like that, so maybe theres are more than 8 bonds. That may explain
> why VMD refuse to load it.
> [...]
> Heyy ??? I've just generated a solvation box of 1.3 Million atoms, with
> "Solvate Plugin".
> I try to load solvate.pdb
> ( ,
> WITHOUT using solvate.psf file, and it works perfectly, with the
> "Determining bond structure from distance search" phase.
> It seems something is wrong with my BigConfig.pdb...
> Any ideas ?
> Thanks in advance
> nicolas
> --
> LMOPS - Lab. Matériaux Organiques à Propriétés Spécifiques
> Bât IUT - Université de Savoie
> Tel: 04-79-75-86-53

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