I'd like to model one of the histidines in my structure to be in a protonated form with hydrogens on the NE2 and ND1. I see there's a param file for protonated histidines (~/rosetta/database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states/HIS_P.params). What's the best way to specify in my pdbfile that I want that particular histidine to be protonated?
I tried renaming the residue to "HIP" in my pdbfile and changing the first few lines of that param file to be:
IO_STRING HIP H
TYPE POLYMER #residue type
But this doesn't work.