I stepped away from this problem for bit, but finally managed to get something working. For those interested there are two solutions I found for inputting a psfgen’d PDB file into Rosetta (directly this results in an error, hence the post title). I am new to this software and file format, so perhaps this already well known.
Problem: CHARMM parameter file used in PSFGEN contains atom aliases that are not readable by Rosetta.
1. The first is just a brute force approach and the first thing I tried: Strip hydrogens from the PDB. Rosetta identifies residues well enough (at least for my proteins), but you lose configurational information of the sidechains.
2. Compare the atom naming from a Rosetta generated PDB with a CHARMM topology file. There are several differences here and you can write a simple script to convert the names of these atoms to Rosetta-friendly versions. For example: HH11 (CHARM) is 1HH1 (Rosetta), as well as delta carbon on ILE and terminal oxygens.
Hope this helps anyone with the same issues.