For me I think two things were going on:
1. A few of the hydrogen names were causing a segmentation fault, for whatever reason.
2. One of the atom types in the PDB was triggering a repacking of some of the sidechains (C or O) because it couldn’t be identified. I need to be sure that the structure of what I’m loading in the pose is maintained, at least until I invoke a particular protocol.
So far scrubbing the PDB seems to be working but may not be the most efficient solution.