Does the pdb file in the output folder of pKa give us the right protonation state of pdb file?
Also, there are two options in pKa program in ROSEI:
1.Pack side chains and protonation states of the residues neighboring the target residue during pKa calculations
2.Pre-pack the side chains and protonation states of all the residues in the input PDB before pKa calculations
which one should we use to get the right protonation state?