Protonate

I developed the automation script after getting one successful dyana->leap->sander run completed. It should have worked correctly, however the same error occurred. FATAL: Atom .R NCYS 1.A HS 14 does not have a type. I have now discovered that I had correctly modified the nomenclature for the cysteine residue's proton on the sulfur atom. I had in fact used HSG as required. That solution was masked because protonate also changes nomenclature and over wrote my fix. Now I have added a sed line:

sed -e 's/ HG /CYS/HSG CYS/' < leap_temp.apdb > leap_temp_pro.pdb

after protonate has updated the file and before leap processes the data

Does anyone know how to make protonate produce nomenclature for leap in the first place. Or at least have tleap recognize the original HG nomenclature?

My concern is that even though my sed line patches the problem, it could cause problems in a future protein that has a CYS at some other location other than the n-terminus. I also know that a serine also labels a proton HG so global substitution will not work.