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Binding free energy for protein-ligand complexes was computed using the g_mmpbsa tool (Kumari, Kumar & Lynn, 2014). We calculated free energy from MD trajectories separately on two periods, 20–25 ns and 45–50 ns, by sampling snapshots at every 100 ps. The binding free energy was calculated as the sum of van der Waal energy, electrostatic energy, polar solvation energy, and the solvent accessible surface area (SASA) energy.
Copyright and License information: ©2021 Bepari and Reza
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