VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Thu Dec 13 2018 - 09:01:46 CST

Big thanks to you and to Chris Mayne.
Best,
Pawel

W dniu 13.12.2018 o 02:15, Gumbart, JC pisze:
> Thanks to Chris Mayne, I have now patched this in VMD, and it will appear in the next release. If you need a fix now, find the appropriate code in fftk_guiInterface.tcl in your installation and replace the appropriate section with the lines provided below.
>
> Best,
> JC
>
> ttk::button $gds.generate.load -text "Load Dihedral Scan LOG Files" \
> -command {
> set glogs [tk_getOpenFile -title "Select LOG File(s) to Load" -multiple 1 -filetypes $::ForceFieldToolKit::gui::logType]
> if { [llength $glogs] == 0 } {
> unset glogs
> return
> } elseif { $::ForceFieldToolKit::Configuration::chargeOptPSF eq "" || ![file exists $::ForceFieldToolKit::Configuration::chargeOptPSF] } {
> tk_messageBox -type ok -icon warning -message "Action halted on error!" -detail "Cannot find PSF file."
> unset glogs
> return
> } elseif { $::ForceFieldToolKit::Configuration::geomOptPDB eq "" || ![file exists $::ForceFieldToolKit::Configuration::geomOptPDB] } {
> tk_messageBox -type ok -icon warning -message "Action halted on error!" -detail "Cannot find PDB file."
> unset glogs
> return
> } else {
> set scanData [::ForceFieldToolKit::DihOpt::parseGlog $glogs]
> ::ForceFieldToolKit::DihOpt::vmdLoadQMData $::ForceFieldToolKit::Configuration::chargeOptPSF $::ForceFieldToolKit::Configuration::geomOptPDB $scanData
> unset scanData
> unset glogs
> ::ForceFieldToolKit::gui::consoleMessage "Gaussian LOG file(s) loaded (Scan Torsions)"
> }
> }
>
>
>> On Dec 12, 2018, at 11:09 AM, Pawel Kedzierski <pawel.kedzierski_at_pwr.edu.pl> wrote:
>>
>> Dear Dr Gumbart,
>>
>> Thank you for the response. I thought that the button "Load Dihedral Scan LOG Files" on the "Scan Torsions" serves the same purpose as "Load LOG Files" at "Water Int" tab, namely to verify whether the scans calculated make sense and do not show any artifact. Having that failed, I didn't expect that reading the same files at the last tab will actually succeed.
>> I have just checked that at the last tab "Opt Torsions" the optimization goes without errors so its only this mysterious button "Load Dihedral Scan LOG Files" which does not work.
>>
>> I'm CC-ing the VMD list in case someone having a similar problem.
>>
>> Gretings,
>> Paweł Kędzierski
>>
>> W dniu 12.12.2018 o 02:53, Gumbart, JC pisze:
>>> Sorry for being slow to reply. Funny enough, that person sent me a google drive link and although I requested permission twice, they never granted it, so I gave up.
>>>
>>> Hm, this is very interesting. I just realized I have no clue what the point of the “Load Dihedral Scan LOG Files” is. Let me consult with my colleague that wrote that part of the code. Normally, after generating the scan inputs and running them, we move on to the last tab, so we haven’t run into it in my lab.
>>>
>>> Best,
>>> JC
>>>
>>>> On Dec 5, 2018, at 10:05 AM, Pawel Kedzierski <pawel.kedzierski_at_pwr.edu.pl> wrote:
>>>>
>>>> Dear Dr Gumbart,
>>>>
>>>> Im writing to you off VMD list, as you requested attachments for some minimal example in this thread:
>>>>
>>>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/30233.html
>>>>
>>>> The final answer was never given in the cited thread and now I encountered the very same error myself. I did load both PSF and PDB files first.
>>>>
>>>> can't read "::ForceFieldToolKit::GenDihScan::psf": no such variable
>>>> while executing
>>>> "if { [llength $glogs] == 0 } {
>>>> unset glogs
>>>> return
>>>> } elseif { $::ForceFieldToolKit::GenDihScan::psf eq "" |..."
>>>> invoked from within
>>>> ".fftk_gui.hlf.nb.genDihScan.generate.load invoke"
>>>> invoked from within
>>>> ".fftk_gui.hlf.nb.genDihScan.generate.load instate {pressed !disabled} { .fftk_gui.hlf.nb.genDihScan.generate.load state !pressed; .fftk_gui.hlf.nb.gen..."
>>>> (command bound to event)
>>>>
>>>> Tried on Ubuntu 2016.04 LTS Linux using VMD 1.9.4a8 and 1.9.4a12 (a year old, but still the latest). I remember FFTK being picky about Gaussian version so I have tried with versions 2009 B.01, D.01 and E.01, and I believe Gaussian 2016 was not yet available a year ago, at least not in our supercomputing center :).
>>>>
>>>> I am a VMD-L subscriber so you can post the answer on the list only.
>>>>
>>>> I am attaching my PSF and PDB files and one of the problematic Gaussian inputs and logs. Tell me if you need more information.
>>>>
>>>> Since FFTK was not able to read the dihedrals off the parameter file, I added two myself - one for the methyl group and one for sulphonamide. But I don't see any apparent reason why would FFTK refuse to read in the dihedrals from my par file, so I attach it also.
>>>>
>>>> I hope you could find some time to look at this and tell if its me doing something wrong, or maybe how it could be fixed.
>>>>
>>>> With regards,
>>>>
>>>> Paweł Kędzierski
>>>>
>>>> <SNA.scan1.neg.gau><SNA.par><SNA_opt.pdb><SNA_opt.psf><SNA.scan1.pos.gau><SNA.scan2.neg.gau><SNA.scan2.pos.gau><SNA.scan1.neg.log.gz><pawel_kedzierski.vcf>
>>
>> <pawel_kedzierski.vcf>