Dear sir and madam,
I have met with the unfavourable addition of 2 Hydrogen atoms onto sulfonamide Nitrogen instead one (NH2 instead of NH) on a ligand during the coupled_moves docking application runs. It is perfomed by the following command:
~/rosetta_src_2020.08.61146_bundle/main/source/bin/coupled_moves.default.linuxgccrelease @Options_coupledmoves.txt -resfile target.res -nstruct 2 -coupled_moves::ligand_mode true -coupled_moves::backbone_mover backrub -number_ligands 1 -ligand_mode true -ligand_weight 1.0 -ntrials 500 -pH:pH_mode true -pH:keep_input_protonation_state true -initial_repack true -save_sequences true -save_structures true -mc_kt 0.6 -boltzmann_kt 0.6
My task consists in prevention of the unfavourable proton addition onto NH group.
I have already assigned the negative charge to the sulfonamide Nitrogen on PyMOL by the following commands:
1) edit EZA//A/EZL`306/N1
2) Build -> Make (pk1) Negative
These results are reflected in the PDB file as "N1-". I tried to use both protonated and unprotonated ligand inputs (anyway, Rosetta will protonate all vacant sites).
I have already inspected the Rosetta software suite and found several flags, these might keep atoms in special protonated states. I have already even tried to use flags -pH_mode true and -keep_input_protonation_state true, but it didn't keep the sulfonamide Nitrogen out from unwanted protonation.
I even tried to specify the Nitrogen atom type in .params file, but it seems as if there is no option to mark the negatively charged Nitrogen neither in "GenericAtomTypes.md" file nor anywhere else. Furthermore, marking Nitrogen atom as sp3-hybridized one (NG3) isn't suitable with any Nitrogens' GenericAtomTypes assignment (such as Nbb, Nhis or smth. else). Which Nitrogen atom_type_name may be compatible with NG3 option?
Would you be kind to tell me how to disable protonation option for Rosetta applications, such as coupled_moves, please?
I will be sincerely grateful for your explanations and I am looking forward to it.