VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 14 2017 - 05:31:14 CDT

On Wed, Jun 14, 2017 at 5:58 AM, János Szövérfi <johhnnyblack_at_gmail.com>
wrote:

> 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
>

​no. the command is part of a package and you probably have not "activated"
that plugin with the "package require" command.
this kind of issue often doesn't show ​when running VMD in graphical mode,
as most plugin packages are "required" during initializing of the GUI
extensions.

axel.

>
> 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--001a114054464215db0551e90db8--