VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sun Apr 12 2020 - 16:03:29 CDT

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> 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