From: Luis Rosales (
Date: Mon Apr 04 2005 - 16:22:28 CDT


I think that the real difference in the vmd behaviour is in the fact that in
one case (your mega-water box) you have a PSF telling VMD bond order and
On the other hand, your BigConfig is only a pdb and vmd have to guess what is
inside the file to determine bond number and order...
So, maybe if you generate the psf for your bigconfig file you wont be having
the warning again.

Hope that this helps,


> When I try to load my "test" big molecule ( 640,000 atoms, grab it
> at http://www.univ-
> , 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
> (http://www.univ-
> 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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