Poltype2 fails for PF6- with "OSError: Bad input file conftest.mol" #90
Description
Hi,
I am trying to generate AMOEBA parameters for PF6- using Poltype2, but the run fails during conformer generation.
PF6- is a common anion in electrolyte simulations, so I wanted to report this in case hydrogen-free inorganic anions are not currently handled correctly.
Input:
- Molecule: PF6-
Observed output:
Wed Mar 4 17:41:53 2026 No hydrogens detected in input file!
Wed Mar 4 17:41:53 2026 Atom Type Classification
Wed Mar 4 17:41:53 2026 Calling: python "/home/nakamura/hasegawa/poltype2/PoltypeModules/lConformerGenerator.py" -i PF6_3D.mol -p /home/nakamura/miniconda3/envs/xtbenv/bin/xtb
Wed Mar 4 17:41:54 2026 Traceback (most recent call last):
File "/home/nakamura/hasegawa/poltype2/PoltypeModules/poltype.py", line 4607, in RunPoltype
poltype.main()
File "/home/nakamura/hasegawa/poltype2/PoltypeModules/poltype.py", line 2165, in main
params= self.GenerateParameters()
File "/home/nakamura/hasegawa/poltype2/PoltypeModules/poltype.py", line 3236, in GenerateParameters
indextocoordslist=self.GenerateExtendedConformer()
File "/home/nakamura/hasegawa/poltype2/PoltypeModules/poltype.py", line 2631, in GenerateExtendedConformer
mol=rdmolfiles.MolFromMolFile(name,removeHs=False)
OSError: Bad input file conftest.mol
Expected behavior:
Poltype2 should either:
- successfully process PF6-, or
- fail gracefully with a clear message if hydrogen-free inorganic anions are not currently supported.
Actual behavior:
The run proceeds to conformer generation and then crashes because conftest.mol cannot be read.
Possible cause:
It looks like the conformer generation workflow may assume an organic molecule / hydrogen-containing molecule, and may not properly handle hydrogen-free species such as PF6-.
Could you please let me know:
- whether PF6- / hydrogen-free inorganic anions are currently supported in Poltype2
- whether this is a known limitation
- whether there is a recommended workaround for such species
Thank you very much.