Molecular dynamics simulation and thermodynamic integration method were used to calculate the absolute binding free energy of the protein-ligand complex. By the molecular transformation method, the interactions between protein (plus solvent) and its ligand are gradually decreased (or increased) into a non-interacting (or full interacting) state. A potential of a body restraint was used to calculate the free energy changes caused by the loss of translation and rotation freedom of the ligand molecule, that is called as the entropy effect. A mutant trypsin (D189G/G226D) and its polar ligand (benzamidine) were selected as a model to study the influence of the interactions between protein and polar ligand on the binding free energy. The calculation result of the absolute free energy for the model complex (－15.5 kJ/mol) is close to the experimental data (－10.5 kJ/mol).