Add options to PMI's topology file to merge it with the topology file used by this module

[shruthivis]

This module uses a topology file with the names of different domains to be optimized, the PDB start and end residue numbers and PDB file names if any, and the resolutions to start with. Many options are similar to PMI's topology file, with a few extra ones added in.
Consider merging this topology file with the one that PMI uses.