I’ll be most thankful if some one can tell me how to insert a deprotonated LYS (LYN in AMBER) as if LYS is inserted into the PDB with only HZ1 and HZ2, Rosetta gives you a protonated (regular, adds the extra hydrogen) Lys at the end in the output design.
A) Rosetta’s energy functions are not likely smart enough to know what to do with the deprotonated LYS anyway – the standard energy function doesn’t have explicit electrostatics. I believe the explicit electrostatics terms will work properly with a deprotonated lys.
There is a deprotonated lysine with the residue type name LYS_D at (database)/chemical/residue_type_sets/fa_standard/residue_types/protonation_states. I don’t know the names for the python commands, but after reading your pose in, you should be able to do something like replace_pose_residue_copying_existing_coordinates(pose, position, LYS_D ) (it’s in core/chemical/util.hh)
Thanks a lot for replaying so quickly. Isn’t there a 3-letter alias for LYS_D ? I just need that lysine to stay depreponderated as the extra hydrogen drives away my substrate(due to sterics and not electronic structure)
I don’t know if pyrosetta comes with a separate database or not – if you open up the file I mentioned in my previous post, you can rename its three letter code to LYD (or whatever), then name the residue in your PDB the same thing; that might work.