As I understand, MM/PBSA method needs three MD trajectories to calculate the binding energy: (1) the complex trajectory; (2) the receptor trajectory; (3) the ligand trajectory. You calculate each energy entity (vdw, electrostatic, etc) for each of the three species (the complex, the receptor and the ligand) from their corresponding trajecotories and obtain the total energy for the three species (G[complex], G[protein], G[ligand]), and then calculate the binding energy with the following formula:
ΔG[binding] = G[complex] − (G[protein] + G[ligand])
However, both g_mmpbsa and GMXPBSA2.1 seem to use only the complex trajectory to calculate all the energy entities for all the three species. Wouldn’t that be wrong?