When calculating solvation free energy using TI, it is necessary to determine the free energy in the solvent phase ( ∂V ∂λ solvent ) and the gas phase ( ∂V ∂λ gas ) separately. Considering the bonded and non-bonded terms in ML are not separable, we need to develop a new protocol to enable TI calculations using ML/MM approach. In our protocol, we assumed the contributions from solute itself in the gas and solvent phases are the same. Under this assumption, we only need to do TI calculations in the solvent phase and the values ∂V ∂λ are calculated without considering the intramolecular energy of the solute. We then estimate the reorganization energy, which accounts for the free energy difference associated with the different conformational ensembles in the gas and solvent phases. We expect that the reorganization energy can mitigate the prediction error due to the above assumption.