VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Aug 04 2020 - 20:26:58 CDT

Hi Valentin,

I cannot reproduce the error - it works fine for me. All I can suggest at this point is to make sure you are using the latest version of VMD (2020-05-29). If you *still* have problems after that, I would suggest trying to do something simpler, like one log file, one dihedral, etc. and see if you can make anything work.

Best,
JC

> On Jul 28, 2020, at 4:07 PM, Valentin Gogonea <v.gogonea_at_csuohio.edu> wrote:
>
> Hi JC:
>
> I finally found a way to include the dihedral angle info in the psf file.
>
> Unfortunately I get the same error when I run the torsion angle optimization in ffTK.
>
> I would appreciate if you can take a look and try to reproduce the error.
>
> I attached a compressed file with all files needed to run the torsion angle optimization and the error log file.
>
> I also took a picture of the ffTK window of the ffTK GUI.
>
> Thank you for your help.
>
> Best,
>
> Valentin
>
> Valentin Gogonea, Ph.D.
> Professor
> Department of Chemistry
> Cleveland State University
> 2121 Euclid Avenue, SI 422
> Cleveland, OH 44115
> Tel: (216) 875-9717
> Fax: (216) 687-9298
> v.gogonea_at_csuohio.edu <mailto:v.gogonea_at_csuohio.edu>
>
>
> <ffTL_torsion_opt.png>
>
>
>
>
>> On Jul 11, 2020, at 7:18 PM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
>>
>> CAUTION: This email originated from outside of Cleveland State University! Do not click links, open attachments or reply, unless you recognize the sender's email address and know the content is safe!
>> You don’t have any dihedrals in your psf file. I’m not sure how you originally made it, but you need to run it through psfgen again. You could do simply
>>
>> readpsf ___.psf pdb ___.pdb
>> regenerate angles dihedrals
>> writepsf ____.psf
>>
>> Best,
>> JC
>>
>>> On Jul 6, 2020, at 8:19 PM, Valentin Gogonea <v.gogonea_at_csuohio.edu <mailto:v.gogonea_at_csuohio.edu>> wrote:
>>>
>>> Hi JC:
>>>
>>> Thank you for your willingness to help.
>>>
>>> I am trying to derive charmm36 parameters for the cysteine sulfur radical. Everything was OK until torsion angle optimization.
>>> I archived the folders with the files, they follow the same structure and naming as in the tutorial. It is 17 MB so I am going to send it from another email account as it my not go through the Cleveland State filter being > 10 MB.
>>>
>>> I attached here to screen shots as you requested.
>>>
>>> Let me know if you need more information.
>>>
>>> Thank you so much,
>>>
>>> Best,
>>>
>>> Valentin
>>>
>>>
>>> Valentin Gogonea, Ph.D.
>>> Professor
>>> Department of Chemistry
>>> Cleveland State University
>>> 2121 Euclid Avenue, SI 422
>>> Cleveland, OH 44115
>>> Tel: (216) 875-9717
>>> Fax: (216) 687-9298
>>> v.gogonea_at_csuohio.edu <mailto:v.gogonea_at_csuohio.edu>
>>>
>>> <Screen Shot 2020-07-06 at 8.06.33 PM.png><Screen Shot 2020-07-06 at 8.08.12 PM.png>
>>>
>>>
>>>
>>>
>>>
>>>> On Jul 6, 2020, at 7:51 PM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
>>>>
>>>> CAUTION: This email originated from outside of Cleveland State University! Do not click links, open attachments or reply, unless you recognize the sender's email address and know the content is safe!
>>>> Hi Valentin,
>>>>
>>>> You might be missing a file or one is misformatted? If you can make your input available to me (if it’s not too large, email works) along with a screenshot of the tab before you hit “run", I can try to reproduce it.
>>>>
>>>> Best,
>>>> JC
>>>>
>>>>> On Jul 5, 2020, at 11:23 AM, Valentin Gogonea <v.gogonea_at_csuohio.edu <mailto:v.gogonea_at_csuohio.edu>> wrote:
>>>>>
>>>>> Hi VMD-users:
>>>>>
>>>>> I am getting the following error when I am using ffTK for torsion angle optimization.
>>>>>
>>>>> Can anybody give me a hint of what can I do to fix it? Below is the full error message.
>>>>>
>>>>> Thank you.
>>>>>
>>>>> Valentin
>>>>>
>>>>> can't read "kList": no such variable
>>>>> can't read "kList": no such variable
>>>>> while executing
>>>>> "list $kList $boundsList"
>>>>> (procedure "::ForceFieldToolKit::DihOpt::pardata2klist" line 24)
>>>>> invoked from within
>>>>> "::ForceFieldToolKit::DihOpt::pardata2klist $dihToFit"
>>>>> (procedure "::ForceFieldToolKit::DihOpt::optimize" line 176)
>>>>> invoked from within
>>>>> "::ForceFieldToolKit::DihOpt::optimize"
>>>>> (procedure "::ForceFieldToolKit::gui::doptRunOpt" line 64)
>>>>> invoked from within
>>>>> "::ForceFieldToolKit::gui::doptRunOpt "
>>>>> invoked from within
>>>>> ".fftk_gui.hlf.nb.dihopt.runOpt invoke "
>>>>> invoked from within
>>>>> ".fftk_gui.hlf.nb.dihopt.runOpt instate !disabled { .fftk_gui.hlf.nb.dihopt.runOpt invoke } "
>>>>> invoked from within
>>>>> ".fftk_gui.hlf.nb.dihopt.runOpt instate pressed { .fftk_gui.hlf.nb.dihopt.runOpt state !pressed; .fftk_gui.hlf.nb.dihopt.runOpt instate !disabled { .ff..."
>>>>> (command bound to event)
>>>>>
>>>>> Valentin Gogonea, Ph.D.
>>>>> Professor
>>>>> Department of Chemistry
>>>>> Cleveland State University
>>>>> 2121 Euclid Avenue, SI 422
>>>>> Cleveland, OH 44115
>>>>> Tel: (216) 875-9717
>>>>> Fax: (216) 687-9298
>>>>> v.gogonea_at_csuohio.edu <mailto:v.gogonea_at_csuohio.edu>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
> <cyrc.tgz><ffTK_error.log>