VMD-L Mailing List

From: János Szövérfi (johhnnyblack_at_gmail.com)
Date: Wed Jun 14 2017 - 05:45:44 CDT

I tried in this way too, don't works.

part of the tcl script:

#!/bin/env wish
..
package require cgtools
::cgnetworking::networkCGMolecule puts 0 BAR A cg_monomer.pdb
aa_ref_monomer.pdb cg_monomer.top cg_monomer.par 10 2000 0.3 0.05 1.0 0.01
1 10.0 -1
..

vmd console output

1.2
invalid command name "::cgnetworking::networkCGMolecule"
Info) Using plugin pdb for structure file cg_monomer.pdb
Info) Using plugin pdb for coordinates from file cg_monomer.pdb
Info) Determining bond structure from distance search ...

2017-06-14 13:31 GMT+03:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:

>
>
> 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.
>>>
>>> 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
>>> *******************************************
>>>
>>>
>>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>