When reading in CHARMM psf files, I experienced problems for certain psf files. I included one, generated by CHARMM-GUI, which does not work as expected (loading with load_psf works fine, but processing this file or saving it with save_psf produces errors):

step3_input.zip

I think the problem is, that _process_lonepair_section is only executed, if there is a MOLNT section, which is sometimes not the case (e.g. when using the openmm option in CHARMM-GUI, like for the example provided above)

tmp = psfsections['MOLNT'][1]
tag_molecules(self)
if len(tmp) == len(self.atoms):
    # We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
    self._process_lonepair_section(psfsections["NUMLP NUMLPH"])

Is there a reason, why if len(tmp) == len(self.atoms): is used for deciding whether the _process_lonepair_section() function is executed or not?
If not, I suggest a check like this:

if len(psfsections["NUMLP NUMLPH"][1]) != 0: