VMD-L Mailing List

From: János Szövérfi (johhnnyblack_at_gmail.com)
Date: Wed Jun 14 2017 - 07:16:03 CDT

 I figured it out after several hours😀

instead of "require package cgtools" (as mentioned in the tutorial
http://www.ks.uiuc.edu/Training/Tutorials/science/coarse-graining/sbcg-tutorial-html/node4.html
)
"package require cgnetworking" is working.

 Thanks for the suggestions!

2017-06-14 13:53 GMT+03:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:

>
>
> On Wed, Jun 14, 2017 at 6:45 AM, János Szövérfi <johhnnyblack_at_gmail.com>
> wrote:
>
>> I tried in this way too, don't works.
>>
>> part of the tcl script:
>>
>> #!/bin/env wish
>> ...
>> package require cgtools
>>
>
> ​cgtools != cgnetworking​
>
>
>
>
>> ::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.
>>>
>>
>>
>
>
> --
> 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.
>