An Efficient Program for End-State Free Energy Calculations

J Chem Theory Comput. 2012 Sep 11;8(9):3314-21. doi: 10.1021/ct300418h. Epub 2012 Aug 16.


MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at with AmberTools, released under the GNU General Public License.