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.
Thanks a lot
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.
B) 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)
Thanks a lot again,
The three letter code is LYS.
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.