From: John Stone (
Date: Wed Apr 06 2005 - 11:18:24 CDT

  I can't comment on the warning messages emitted by MSMS,
I'd suggest emailing questions like those to the
Michel Sanner, the author of MSMS. Perhaps this should be an
FAQ on the MSMS home page or something since I'm sure others would
like to know what those messages mean. Those aren't VMD messages,
even though they appear in the VMD console, they are actually all from MSMS.
Michel's email address is on the MSMS home page as I recall.

I'll let you know when I figure out what's going on with your "bigconfig"

  John Stone

On Wed, Apr 06, 2005 at 06:10:12PM +0200, Nicolas CHARVIN wrote:
> >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.
> after installing MSMS (sorry :)... MSMS 2.5.5 by the way:
> virus-simple.vmd loads fine with VDW by default, but when I choose MSMS, I
> get many "WARNING: geodesic which intersects odd number of edges" and
> "ERROR: find_SES_contact_faces: inf==0 for face 362942", and so on.
> Finally, vmd says "failed to compute level 0 surface, try again 2"
> virus.vmd (there is no virus-large.vmd on your website) loads, with many
> "WARNING: geodesic which intersects odd number of edges" during the MSMS
> generation. But it works. I cannot tell you the FPS since it's white
> background, but it is approx. 1 fps, and 646 MB of RAM usage.
> virus-faster.vmd loads, with "WARNING: Genus mismatch" messages. And it
> rotates more smoothly, approx 2 fps, and 413 MB of RAM usage.
> Concerning "BigConfig.pdb"
> >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
> right! It is no biological thing, it is only 640 * 1000 CH2. Please do not
> ask me more details ;). I've attached a picture of this molecule under
> Qmol (BigConfig_under_Qmol.gif).
> Thanks a lot for your help
> nicolas

> --
> LMOPS - Lab. Matériaux Organiques à Propriétés Spécifiques
> Bât IUT - Université de Savoie
> Tel: 04-79-75-86-53

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