I used molfile_to_params.py to create .params files for the two substrates for 'my' protein. I'd like to relax the modeled structure with these compounds present. I found that leaving these files in the current working directory wasn't right - relax still crashes because it doesn't recognize the residue. Copying the .params files into rosetta_database/chemical/residue_type_sets/fa_standard/residue_types wasn't right either, or wasn't enough. What else should I be doing?
The more appropriate method is the flag -extra_res_fa , which adds your params files to that one run of rosetta.
The permanent method is to add the files to the residue type sets where you added them, but ALSO add them to residue_types.txt in osetta_database/chemical/residue_type_sets/fa_standard/. (That list controls which of the residue types actually get read in - some are around for use but not defaulted to active.)