VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Wed Jun 18 2025 - 18:09:01 CDT

Hi Hanna,

Sorry for not seeing this until now! Can you please send me the files separately so that I can reproduce the error?

Best,
JC

> On Jun 10, 2025, at 11:29 AM, Hanna Baltrukevich <hanna.baltrukevich_at_pharmazie.uni-marburg.de> wrote:
>
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>
> Dear VMD community,
>
> I am trying to obtain new parameters for a small organic molecule with
> ffTK (via VMD 2.0.0a5) and PSI4 (1.9.1).
>
> I have successfully generated dihedral scan input and run all the
> scripts without issues with PSI4. I am able to visualize the
> trajectory containing seven conformations, each corresponding to one
> out of the seven dihedral scan steps via "Load Dihedral Scan Output
> Files" (using .out files from PSI4). However, if I try to load the
> same .out file in the "Torsion Explorer", I receive this error:
>
> can't read "vmd_frame(90)": no such element in array
> can't read "vmd_frame(90)": no such element in array
> while executing
> "list $vmd_frame($molid) $vmd_frame($molid)"
> (procedure "::ForceFieldToolKit::GenDihScan::TorExplor::plotData" line 11)
>
> Upon clicking "OK" in the error window, a new molecule appears in the
> main window, and, indeed, it has 0 frames. However, when I load into
> this molecule the .xyz file (containing the coordinates extracted from
> the mentioned above .out file), I can use "Analyze Trajectory" in
> "Torsion Explorer" window, which extracts the indices, types and
> angles. Nevertheless, I still cannot obtain the graph using "Torsion
> Explorer".
>
> It seems that "Torsion Explorer" is unable to directly extract the
> coordinates from .out files generated by PSI4. Is there a solution to
> this issue, maybe changing file formatting?
>
> Thank you very much in advance for any help!
> Best wishes,
> Hanna
>
>
>
>
> --
>
> Hanna Baltrukevich
> PhD student at the Prof. Peter Kolb group
> Institut für Pharmazeutische Chemie
> Philipps-Universität Marburg
>