VMD-L Mailing List

From: Nicolas CHARVIN (Nicolas.Charvin_at_univ-savoie.fr)
Date: Wed Apr 06 2005 - 11:10:12 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.

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 


--
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
BigConfig_under_Qmol.gif