VMD-L Mailing List

From: Dive, Aniruddha Mukund (aniruddha.dive_at_wsu.edu)
Date: Wed Feb 21 2018 - 12:18:02 CST

Thanks John for your suggestion,

I understand the use of $env(VARIABLE) prior to launching VMD. To avoid the use of that I am writing the value of variable to a "tmp" file and then I read the value of variable from the "tmp" file in the TCL script. I am able to successfully read the value of the variable from the tmp file in the TCL script. The error I face is that VMD is not able to load the trajectory file through the below command in the TCL Script

mol load pdb Si_S_config$data.pdb

Below is the error I get with the attached TCL Script:

file16
2
2
2
2
2
2
2
2
2
2

Si_S_config2
2
2
2
2
2
2
2
2
2
.pdb
ERROR) Could not read file Si_S_config2
ERROR) 2
ERROR) 2
ERROR) 2
ERROR) 2
ERROR) 2
ERROR) 2
ERROR) 2
ERROR) 2
ERROR) 2
Unable to load structure file Si_S_config2
2
2
2
2
2
2
2
2
2
.pdb
There is no 'top' molecule in atomselect's 'molId'

The file name I want to load is Si_S_config2.pdb, but somehow the file name ends after$data and it doesnot read the filename as Si_S_config2.pdb but instead as Si_S_config2 and .pdb separately. Kindly let me know how to get around this issue? Is this issue due to non declaration of $env(VARIABLE)?

Regards,

Aniruddha M Dive

PhD student

School of Mechanical and Materials Engg.

Washington State University

________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Tuesday, February 20, 2018 8:49:00 AM
To: Dive, Aniruddha Mukund
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: VMD TCL Script to save last frame of a trajectory using bash+tcl scripts

Hi,
  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
  vmd_at_ks.uiuc.edu

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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