2.11. Binding free energy calculation using MM-PBSA

MMPBSA (Molecular Mechanics Poisson-Boltzmann surface area) method is widely used to calculate the binding free energy to predict the stability of the protein-ligand complex after MD Simulation (Kumari et al., 2014). Binding free energy calculations consist of free solvation energy (polar and non-polar solvation energies) and potential energy (electrostatic and Vander Waals interactions). Here, binding free energy calculations of protein-ligand complexes were done by the MMPBSA method. The MD trajectories were processed before doing MM-PBSA calculations for the last 10 ns. Then average binding energy calculations were done with ‘python’ script provided in g_mmpbsa.