Abstract: In many predictive tasks accurate free energy estimation is needed. The molecular mechanics/ Poisson- Boltzmann solvent accessible surface area (MM/PBSA) approach has proven to be one of the most accurate. However, the correlation between the estimated free energy and the distance (e.g. root mean square deviation (RMSD)) from the most stable conformation is hindered by the strong free energy dependence on minor conformational variations. In the present paper a protocol for MM/PBSA free energy estimation is designed and tested successfully on several loop decoy sets. Further integration of MM/PBSA free energy estimator with the "colony energy" approach makes the correlation between free energy and RMSD from the native structure apparent, thus making the method both accurate and robust.