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.
The one thing you're missing is that reading in protonated variants isn't enabled by default. Try adding the options "-keep_input_protonation_state" and "-pH_mode" to your commandline. (It's probably missing the latter, more than the former, that's hurting you with your renamed file: if it's not set, Rosetta ignores everything in the protonation_states directory.)
I still can't seem to get this to work. I've tried using your suggestion (version 1 in my flags below) or specifying "extra_res_fa" and a protonated param file (version 2). The only difference between this param file and the one in the rosetta database is that I changed "IO_STRING HIS H" to "IO_STRING HIP H". I renamed the histidine in my pdbfile to "HIP". Input pdb and modified params file are attached. (NOTE: I also tried changing the HIS_P.params in the rosetta database to have the same "IO_STRING HIP H" line).
# === Version 1 === #
# === Version 2 === #
I wanted to run a protonated histidine too. So I gave this a spin and got errors. One of the warning was that the HIP did not have a specified chirality, so I added the L_AA to the property line and inexplicably all worked. I did not change the geometry as suggested in another post. I have attached my HIP.params (remove the txt, which is there for upload reasons).