VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 05 2005 - 17:31:38 CDT

Try using the other .vmd files, virus-small.vmd and then virus-large.vmd
and see if those work on your machine. Let me know if you get the MSMS
surface as it should be.

  John Stone
  vmd_at_ks.uiuc.edu

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
> http://www.univ-savoie.fr/labos/lmops/people/ncharvin/bazar/BigConfig.zip)
> , 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-savoie.fr/labos/lmops/people/ncharvin/bazar/solvate.zip) ,
> 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
>
> --
> Nicolas.Charvin_at_univ-savoie.fr
> LMOPS - Lab. Matériaux Organiques à Propriétés Spécifiques
> Bât IUT - Université de Savoie
> 73376 LE BOURGET DU LAC CEDEX
> Tel: 04-79-75-86-53
>
> http://www.univ-savoie.fr/labos/lmops
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078