From: János Szövérfi (johhnnyblack_at_gmail.com)
Date: Wed Jun 14 2017 - 04:58:06 CDT

I ran the script with

vmd -dispdev text -e vmd_script.tcl

from the script.sh and the error invalid command name
"::cgnetworking::networkCGMolecule"
is displayed in vmd.

I think that vmd cant read the whole
::cgnetworking::networkCGMolecule puts 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
command, only what's in front of puts

2017-06-14 12:50 GMT+03:00 Fotis Baltoumas <fbaltoumas_at_biol.uoa.gr>:

> 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::networkCGMolecule puts 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.grhttp://biophysics.biol.uoa.grhttp://bioinformatics.biol.uoa.gr
> *******************************************
>
>