Molecular dynamics simulations up to 10 ns are carried out to study binding of inhibitor to HIV-1 protease using standard AMBER force field and polarized protein-specific charge (PPC). Binding free energy was calculated by MM/PBSA method.PPC is derived from quantum mechanical calculation for protein in solution and therefore it includes electronic polarization effect. It shows that binding free energy calculated with PPC charge is closer to experimental result than that with AMBER force field.