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Calculation of binding free energy using Poisson-Bolzmann surface area (MM-PBSA)
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The Poisson-Boltzmann or generalized Born and surface area continuum solvation (MM-PBSA or MM-GBSA) is a method for the calculation of the ligand affinity for proteins [44]. The binding free energy of the protein-ligand complexes (PsGH3 + cellobiose and PsGH3 + celloheptaose), was calculated from their last stable 20 ns trajectories. The tool “g_mmpbsa” with default parameters [43] was utilized for potential energy and solvation free energy calculations.
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