Hey all :)
Does the Rosetta force field incorporate parameters for PTMs such as hydroxyproline and C-terminal amidation? If so, where can I see this in the database? If not, how can I parameterize this?
Rosetta/main/database/chemical/residue_type_sets/fa_standard/patches is where parameters for the altered types are stored. "patches" indicates that these are modifications of base ResidueTypes (which are instantiated from parameters in the sibling directory residue_types). Both of the chemistries you are asking about seem to be there, based on the file names.
Getting Rosetta to read those modifications in can be tricky, as you have to have atoms named exactly as the patch expects.