Cassandra is not really designed for such large systems, but you can give it a try. I think editing the pdb by hand will be very challenging. You should try out a new set of tools that have been developed for Cassandra called MosDeF Cassandra. There are tools for automatically building and assigning force fields. We haven't tried these for proteins, but you can give it a shot.
github.com/MaginnGroup/mosdef_cassandra
