Chimera or other software to perform protonation states of a protein

I want to perform a Molecular Docking between some ligands and a protein in different pH conditions.

For this, I calculated the distance between atoms in different pH concentrations for the ligands, using the software Avogadro.

I would like to do the same with my protein, that is, get the structure and its protonation state for two different pHs.

Is there any software that allows me to do that?