I have a protonated GLU in the active site of an enzyme. I would like to use GLU_P1.params in my simulation by -extra_res_fa (the OE2 is protonated). I need to change the name of this protonated GLU in the PDB, but I am not sure what it should be. Because the NAME and IO_STRING are different and are not three letter code. Please see below and let me know what the name of this protonated GLU in the PDB file should be.
#rosetta residue topology file
#neutral GLU by Krishna
#partial charges from CHARMM27
IO_STRING GLU E
TYPE POLYMER #residue type
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:
Best of luck!