VMD/psfgen scripting: undefined variable

From: Richard Baxter (Richard.Baxter_at_utsouthwestern.edu)
Date: Thu Nov 08 2007 - 22:30:12 CST

Dear All,

Can anyone explain the following to me? An interactive vmd session:

kong <10:21pm> 126% vmd -dispdev text
Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
..
vmd > set x 10
10
vmd > puts "the value of x is $x"
the value of x is 10
vmd > quit
Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
Info) Exiting normally.

Now try putting it in the following script:
setup vmd
which vmd
vmd -dispdev text <<END
set x 10
puts "the value of x is: $x"
quit
END

and you get:
kong <10:21pm> 127% ./test.com
/usr/progs/vmd-1.8/bin/vmd
Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
..
10
the value of x is:
Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
Info) Exiting normally.

Let's try an interactive psfgen session:
kong <10:24pm> 129% psfgen
PSFGEN from NAMD 2.6 for Linux-i686
% set x 10
10
% puts "the value of x is $x"
the value of x is 10
% exit

Now put that in a script:
setup namd
which psfgen
psfgen <<END
set x 10
puts "the value of x is: $x"
exit
END

and you get:
/usr/progs/NAMD_2.6_Linux-i686/psfgen
PSFGEN from NAMD 2.6 for Linux-i686
the value of x is:
kong <10:25pm> 132%

At least the vmd script spat out the value of x, but didn't call it.
PSFGEN didn't even return the variable value when set! I am at a loss to
explain, expecially since I already went through the VMD and NAMD
tutorials and those scripts worked fine.

Help!

Richard

-- 
Richard Baxter <Richard.Baxter_at_UTSouthwestern.edu>
Howard Hughes Medical Institute

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