VMD-L Mailing List

From: _at_huji.ac.il
Date: Sun Feb 04 2007 - 02:21:02 CST

Justin Hi!
I want to thank you. It is really worked. I was missing this "-args" flag.
Thanks again
Regina
John Stone wrote:
> Justin asked me to forward this on, as his web mail client
> had trouble with your address:
>
>> Hi,
>>
>> In case the email John mentioned doesn't solve your problem, it seems
>> that you're also missing the required "-args" option to send command
>> line arguments to a script. See this message:
>>
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5438.html
>>
>> Cheers,
>> Justin
>>
>
>
>
> On Thu, Feb 01, 2007 at 09:39:20PM +0200, " politr"@huji.ac.il wrote:
>
>> Dear VMD users and developers,
>> I'm interested to call my tcl script from perl when I want to transfer
>> some arguments to tcl. How can I do it?
>> Let say I want to transfer name of the file and in tcl script I want to
>> open this file for writing. Does anybody knows how to do it?
>> In the code attached I have also sent psf and dcd name and it is working
>> but when I'm trying to send an addition argument (name) it doesn't work
>> as well as as I can't use argument to open file for writing. All the red
>> part is not working. I hope somebody can hep me. Thank you very much.
>> Regina
>>
>> set psf [lindex $argv 0]
>> set dcd [lindex $argv 1]
>> set psf_filename $psf
>> set dcd_filename $dcd
>> mol load psf $psf_filename
>> animate read dcd $dcd_filename waitfor all
>> set peptide [atomselect top protein]
>>
>> set name [lindex $argv 2]
>> set pdb_peptide /usr/people/$name
>> animate write pdb $pdb_peptide beg 0 end $final_frame waitfor all sel
>> $peptide
>>
>> set sasa_file_name [lindex $argv 3]
>> set sasa_file [open /usr/people/$sasa_file_name w]
>>
>> from perl:
>> vmd -dispdev text -eofexit < my.tcl $psf_name $dcd_name $name
>> $sasa_file_name> output.log
>>
>
>