From: John Stone (
Date: Tue Feb 20 2018 - 10:49:00 CST

  You need to use Tcl's $env(VARIABLE) interface to obtain environment
variables set in external command shells prior to launching VMD.
Similarly, when using bash/bourne shells, you will need to use
"export FOO=BAR" to ensure that the variable propagates to subshells
and child processes like the VMD instance(s) you want to run.

Best regards,
  John Stone

On Mon, Feb 19, 2018 at 10:37:33PM +0000, Dive, Aniruddha Mukund wrote:
> Hi All,
> I am trying to make a bash script which will traverse through various
> directories and save the coordinates of the last frame from a trajectory
> in each of the directory. I have made a bash script attached hereby to
> help me traverse through different directories and along with that I have
> made another tcl script to save the coordinates of the last frame from the
> trajectory. The TCL script works fine without the variable introduced
> while loading the molecule. But when I introduce a variable in the name of
> the molecule in the TCL script, the script is not able to recognize the
> molecule and hence cannot load the molecule.
> Kindly let me know what could be a possible reason for this?
> Aniruddha M Dive
> PhD student
> School of Mechanical and Materials Engg.
> Washington State University

> set f [open tmp]
> set data [read $f]
> close $f
> puts "Si_S_config$data.pdb"
> mol load pdb Si_S_config$data.pdb
> [atomselect top all frame last] writepdb Si_S_config_$data.pdb

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