To my knowledge, params files for protonated amino acids are made accessible with the ‘-pH_mode’ options. When changing the pH in a system, the residues are still the same (glutamate is glutamic acid, histidine is histidine, etc.), so the convention in Rosetta is to keep the same naming scheme.
However, using the pH option will alter the protonation states of other amino acids in the protein and the one in the active site. It sounds like you only want to change the protonation state of one particular residue while the others remain at a neutral pH. I’ve accomplished this in the past with the following setup:
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copy the params file for GLU_P1 locally
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edit the params file to create a “custom” residue
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change the IO_STRING to something unique, like ‘GLP E’. Note that GLP might not be unique. You could use EP1 or GP1.
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add the line ‘ROTAMER_AA GLU’ to allow this residue to access the standard glutamate rotamer library (see Rosetta/main/source/src/core/chemical/residue_io.cc for more info on params file options.)
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edit the protonated residue in the input PDB, so the three-letter code is GLP instead of GLU
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supply your “custom” params using -extra_res_fa as you had thought to do originally.
Best of luck!
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