I looked into the problem with openbabel 3 a bit more (see https://github.com/alanwilter/acpype/issues/10) and I saw acpype is performing the PDB -> MOL2 conversion with the babel command rather than obabel. The former was removed in v3. This small change is enough to get acpype working for me with openbabel 3.
simonbray
commented
4 years ago
I looked into the problem with openbabel 3 a bit more (see https://github.com/alanwilter/acpype/issues/10) and I saw acpype is performing the PDB -> MOL2 conversion with the
babelcommand rather thanobabel. The former was removed in v3. This small change is enough to get acpype working for me with openbabel 3.