VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 12 2005 - 10:20:08 CST

Hi,
  I'm guessing that Insight's startup script is causing problems due to
one of the following possible reasons:
- Changing these two environment variables:
   LD_LIBRARY_PATH
   LD_ASSUME_KERNEL

- An error in the insightII startup script is causing csh to error out
  before it is finished processing your login scripts, this too can
  give problems in some cases.

One solution to insightII causing problems might be to separate it's
stuff from your main login files. I.e., move the source accelrys stuff
into a new "insightII" script and have that script start insightII. If
insightII isn't working for you either, perhaps there's something wrong
there that needs fixing anyway, in which case I'd focus on solving that.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 12, 2005 at 02:36:57PM +0200, Dr. Daniel James White PhD wrote:
> Hi John and Axel
>
> here is some more informationa bout the insightII cshrc
> that makes vmd crash on linux
>
> might hold the key?
>
> cheers
>
> Dan
>
>
> Begin forwarded message:
>
> >
> >>also I have noticed that the insightII cshrc file causes VMD to crash.
> >>to run VMD I have to disable the source accelrys cshrc line in my
> >>.cshrc for VMD to launch.
> >>
> >>this means there is some thing bad in the accelrys cshrc which is
> >>bombing the c shell somehow..............
> >
> >The .cshrc is mainly just defining some environment variables.
> >At least the following ones are defined or changed.
> >
> > BCL
> > BIOSYM
> > BIOSYM_CONTEXT
> > BIOSYM_LIBRARY
> > BIOSYM_PLATFORM
> > BIOSYM_ROOT
> > DELPHIDATA
> > FASTLIBS
> > FORCEFIELD
> > INSIGHT_POTENTIAL_TEMPLATES
> > LD_LIBRARY_PATH
> > LD_ASSUME_KERNEL
> > LM_LICENSE_FILE
> > MSI_LICENSE_FILE
> > MSI_LIC_PACK_DIR
> > MSI_LIC_PLATFORM
> > MSI_LIC_WEBLAB_LOG
> > PATH
> > RESIDUE_LIBRARY
> > STEREO_DEVICE
> > STEREO_TRIGGER
> >
> >If VMD uses some of these variables, then it may be the source of the
> >errors. I guess the LD_ASSUME_KERNEL might by the most potential
> >candidate, if VMD wants to use LD_ASSUME_KERNEL 2.4.20 and
> >insight 2.4.19.
> >
> Dr. Daniel James White BSc. (Hons.) PhD
> Bioimaging Coordinator
> Nanoscience Centre and
> Department of Biological and Environmental science
> Division of Molecular Recognition
> Ambiotica C242
> PO Box 35
> University of Jyväskylä
> Jyväskylä FIN 40014
> Finland
> +358 14 260 4183 (work)
> +358 468102840 (mobile)
>
> http://www.chalkie.org.uk
> dan_at_chalkie.org.uk
> white_at_cc.jyu.fi
> 

-- 
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