VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Fri Apr 17 2020 - 18:03:45 CDT

Hi Andrej,

Sorry for taking a while to get back to you. After trying to track down the bug, I realized it was quite simple actually - your psf doesn’t have any dihedrals! At some point you should have used psfgen to generate it, which should add all the angles and dihedrals. When in doubt (and probably always to be safe), you can include the line “regenerate angles dihedrals” before the writepsf and writepdb lines of your psfgen script.

Best,
JC

> On Apr 12, 2020, at 7:10 PM, Andrej Tekel <nio9998_at_gmail.com> wrote:
>
> Thank you for your fast response. I am using VMD 1.9.3, have been using 1.9.4 but I also had an error (different one, probably related to my pc) with opt. torsions section. I cant send all pes log files, hope it does not matter.
> Best regards,
> Andrej T
>
> ne 12. 4. 2020 v 23:03 odesílatel JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> napsal:
> Hi Andrej,
>
> Please prepare a minimal set of files and send it to me to see if I can reproduce the error.
>
> Also, which version of VMD are you using?
>
> Best,
> JC
>
> > On Apr 12, 2020, at 4:32 AM, Andrej Tekel <nio9998_at_gmail.com <mailto:nio9998_at_gmail.com>> wrote:
> >
> > Hello,
> > I am optimizing parameters for two ligands. During parametrization of dihedrals for one of them, I am getting this error after clicking optimize in Opt. torsions section of fftk.
> > can't read "kList": no such variable
> > while executing
> > "list $kList $boundsList"
> > (procedure "::ForceFieldToolKit::DihOpt::pardata2klist" line 24)
> > invoked from within.........
> > After I checked debugging log of fftk, I found out that although input section seems fine( the same as in one that worked) until the end of QM load data section. After that there is " Dihedral definitions to be
> > constrained and optimized" section, which is empty.
> > The only difference between two ligands I am aware of, is that dihedrals for the working one were loaded automatically, from read from par button. Read from par did not work for the second one, so I added them manually. I checked whether angles are properly by loading log files as a trajectory and simply observing what bonds are rotating and indeed these are also good so I really dont know what I am missing. Thank you for any kind of help.
> > Andrej Tekel
>
> <UNK.analogy.par><optneprot.pdb><neprot-opt2.psf><par_all36_cgenff.prm><UNK.scan1.neg.log><UNK.scan1.pos.log>