GROMACS version:4.5.3
GROMACS modification: Yes
Why do we want the residue to be protonated, if it’s pka value is close to the ph we want to simulate in?
If a residue’s pKa value is close to the pH, that does not mean it is protonated. That means its protonation state is hard to define. If pKa = pH, the residue is protonated 50% of the time (or better stated, 50% of equivalent residues in the system are protonated). A residue is considered predominantly protonated when its pKa is below the pH.