VMD-L Mailing List

From: Valentin Gogonea (v.gogonea_at_csuohio.edu)
Date: Tue Aug 04 2020 - 21:17:02 CDT

Thank you JC.

Fortunately I realized that I was inputing the indices of atoms instead of atom types. Once I entered the correct input it worked.

Sorry for waiting your time.

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

> On Aug 4, 2020, at 9:26 PM, JC Gumbart <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,
>
> 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 <mailto: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 I’m not sure how you originally made it, but you need to run it through psfgen again.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>
>