VMD-L Mailing List

From: Hanna Baltrukevich (hanna.baltrukevich_at_pharmazie.uni-marburg.de)
Date: Tue Jun 10 2025 - 10:29:48 CDT

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