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Most molecules contain some specific functional groups likely to loose or gain a proton under specific circumstances. Each ionization equilibrium between the protonated or deprotonated forms of the molecule can be described with a constant value called pKa. The pKa plugin calculates the pKa values of all proton gaining or loosing atoms on the basis of the partial charge distribution.
There is no upper limit for the number of ionizable atoms in the molecule and so the pKa Plugin can also be used for proteins.
Learn more about how the plugin calculates pKa.
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