I want to know the protonation state of some pdb ligands. For example, on the ligand, I want to know if the nitrogen is in its tertiary or quaternary form. I have been looking on the structure page and on the validation report without success. I am thinking about deriving the protonation state from the ph information of the structure environment, in this case 7.2. But I am not sure if this make sense.
In general, you have to decide the system pH for which you want to do the simulations, then, use a tool to protonate your system accordingly.
The choosing of the pH will depends on the type of system, applicability, physiology, etc. For example, you could simulate a protein in physiological conditions (pH 7.2) but also simulate the behavior of the same protein in a sensor that works at different pH. In this case, you have to protonate two times.