In this review of MM/PBSA method, Wang et al. analyze every component of the approximation using MD simulations. They show that the nature of this method is the calculation of binding free energy in aqueous solution of the system. From here, the compute of the solvation free energy is separated in two components, polar and nonpolar. In this study, the use of the modern nonpolar model improved the RMSD's of relative binding affinities. In order to solve PB equations, they employed the finite-difference Poison-Boltzmann method, using, concluding that a spacing of 0.5 Å is a good value to use, although electrostatic binding free energies depend on the grid spacing used. The choices of atomic and solvent probe radii is discussed too. Also, select the correct solute dielectric has been reaffirmed. Finally, an absolute binding free energy calculations comparison is made.
In this review of MM/PBSA method, Wang et al. analyze every component of the approximation using MD simulations. They show that the nature of this method is the calculation of binding free energy in aqueous solution of the system. From here, the compute of the solvation free energy is separated in two components, polar and nonpolar. In this study, the use of the modern nonpolar model improved the RMSD's of relative binding affinities. In order to solve PB equations, they employed the finite-difference Poison-Boltzmann method, using, concluding that a spacing of 0.5 Å is a good value to use, although electrostatic binding free energies depend on the grid spacing used. The choices of atomic and solvent probe radii is discussed too. Also, select the correct solute dielectric has been reaffirmed. Finally, an absolute binding free energy calculations comparison is made.