openff-toolkit: Problem generating proper topology using either ParmEd or PDBFile

I’m trying to go from AMBER formatted file to OEMols and topology. I’ve figured out how to get to the OEMols using PDB as an intermediate format. However, I’m still having issues with the topology. I’m using the GitHub release of openforcefield (reporting version 0.0.3 through pip). I think this gist summarizes the issue: https://nbviewer.jupyter.org/gist/slochower/d319634570c45cb8a5c1bb7916fc5456