Bug Report: Incorrect Aromatic Ring Detection and Parameter Assignment #82
Description
When running poltype2 with the attached PC.sdf structure and poltype.ini, the program incorrectly identifies non-aromatic sp² carbon atoms as part of a benzene ring and assigns generic benzene torsion parameters in the generated final.key.
input Information
structure=PC.sdf
numproc=8
maxmem=16GB
maxdisk=50GB
rotalltors=True
Observed Behavior
In the generated final.key, the following torsion parameter is assigned:
# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [405, 406, 404, 402] = [[11], [12], [10], [5]]
torsion 405 406 404 402 -0.67 0.0 1 6.287 180.0 2 0 0.0 3
This suggests that atoms [405, 406, 404, 402] were interpreted as part of an aromatic ring (specifically, benzene), although the molecular structure in PC.sdf contains no aromatic rings.
Moreover, at least three other torsions involving non-aromatic environments are also incorrectly assigned benzene-derived torsion parameters.
Expected Behavior
poltype2 should correctly distinguish between generic planar sp² systems and aromatic rings.
Benzene torsion parameters should not be transferred to non-aromatic systems.
Planarity should be enforced via appropriate constraints or parameters, but not via other ways.
Attached Files
PC.sdf: initial structure
poltype.ini: input settings
final.xyz: optimized geometry
final.key: output parameter file
bug.zip
Request
Please investigate the aromatic ring detection logic in poltype2. A more robust method to differentiate aromaticity (e.g., via bond orders or aromatic flags in the input file) would help avoid incorrect torsional parameter assignments.
Technical Question
In addition, I would like to ask:
What kind of potential or energy terms are used in TINKER/Poltype2 to enforce or maintain the planarity of sp² carbon environments (e.g., around C=O bonds)?
Understanding this would help clarify whether planarity is preserved by angle terms, torsional terms, improper dihedrals, or other specific treatments.