VMD-L Mailing List

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Wed Jun 14 2017 - 04:50:49 CDT

Hello,

This may sound a bit stupid but, are you actually calling the vmd
executable in your bash script? CGnetworking, as well as all other vmd
commands are not part of the standard Tcl packages, they work only
through vmd itself.

I would suggest you should include in your script the following:

vmd -dispdev text -e script.tcl

and put the ::cgnetworking:: command and its arguments inside script.tcl.

Hope I helped,
Fotis

On 06/14/2017 11:26 AM, János Szövérfi wrote:
> Hi!
>
> I'm writing a bash script which executes a vmd/tcl script.
> My problem is that i want to execute the CG builder within the script :
>
> "#!/bin/env wish
> .....
> ::cgnetworking::networkCGMoleculeputs 0 BAR A cg_monomer.pdb
> aa_ref_monomer.pdb cg_monomer.top cg_monomer.par 15 3000 0.3 0.05 1.0
> 0.01 1 10.0 -1
> ...."
>
> However when I run the script it doesn't recognize the command:
> invalid command name "::cgnetworking::networkCGMolecule"
>
> I think that the problem is the "puts" command, which is also tcl
> command.
>
> Is there a way to escape the puts or what could be the solution?
>
> Thanks
>
> 

-- 
*******************************************
Fotis A. Baltoumas
Phd Candidate, Bioinformatics Postgraduate Programme
Department of Cell Biology and Biophysics
Faculty of Biology, University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
*******************************************