VMD-L Mailing List

From: Dr. Daniel James White PhD (dan_at_chalkie.org.uk)
Date: Wed Jan 12 2005 - 01:33:05 CST

Hi,

There seems to be a conflict between InsightII from acellrys,
  and VMD

InsightII requires that the following cshrc file is sourced before
insightII is launched
so I was instructed to put a line in my .cshrc to source this file

this is what causes vmd to fail
I wouldn't be surprised is there is a problem here as the linux support
for InsightII from accelrys is very new – it's not even working at the
moment for some odd reason ( although before Xmas it was...... fedora
core 3 self updates likely to be the problem there, but I digress....)

any clues ?

Dan

# cshrc
# Environment definition script for Accelrys software.
#
# Place the following line in the ~/.cshrc file of any user
# desiring to use Accelrys software products:
#
# source /usr/msi/cshrc
#
# Accelrys Inc. 2001
#---------------------------------------------------------------

source /home/dan/Desktop/insightII/cdrom/License_Pack/msi_lic_cshrc

# Set the BIOSYM_ROOT environment variable to point to the root
# of the Installation tree and set BIOSYM_CONTEXT to the default
context.
setenv BIOSYM_ROOT /usr/local/accelrys
if ($?BIOSYM_CONTEXT == 0) setenv BIOSYM_CONTEXT I2000.3

# Set up additional interactive environment variables.
setenv BIOSYM ${BIOSYM_ROOT}/${BIOSYM_CONTEXT}
setenv BIOSYM `echo $BIOSYM | sed 's%//%/%g' `
#source $BIOSYM/config/special/cshrc_platform # Set BIOSYM_PLATFORM

# Create set_biosym_context alias
alias set_biosym_context \
   'setenv setcontext_arg "\!:*"; source $BIOSYM_ROOT/biosym_setcon'

# Create set_context alias
alias set_context \
   'setenv setcontext_arg "\!:*"; source $BIOSYM_ROOT/biosym_setcon'

alias reset_env \
   'setenv setcontext_arg $BIOSYM_CONTEXT; unsetenv BIOSYM_CONTEXT;
source $BIOSYM_ROOT/biosym_setcon'

# Use biosym_setcon to define context
setenv setcontext_arg $BIOSYM_CONTEXT
setenv BIOSYM_CONTEXT Undefined
source $BIOSYM_ROOT/biosym_setcon

On 11 Jan 2005, at 18:50, Axel Kohlmeyer wrote:

>
>>>> "DW" == Daniel James White PhD <Dr.> writes:
>
>
> dan,
>
> this check is easy. just rename your .cshrc to .disabled.cshrc
> or something else and try again. for some setups you have to
> log out and back in to have this change take full effect.
>
> axel.
>
>
> DW> Hi John,
>
> DW> I have stuff added to my .cshrc file for insightII
>
> DW> I can start csh and tcsh
> DW> with no errors output to the terminal....
>
> DW> so how do I check if something really is bombing but the shell isnt
> DW> telling me?
>
> DW> Dan
>
>
> [...]
>
>
>
> --
>
> =======================================================================
> Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>
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