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      MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.

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          Abstract

          MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py 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 MMPBSA.py, 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. MMPBSA.py 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 http://ambermd.org/ with AmberTools, released under the GNU General Public License.

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          Author and article information

          Journal
          J Chem Theory Comput
          Journal of chemical theory and computation
          1549-9618
          1549-9618
          Sep 11 2012
          : 8
          : 9
          Affiliations
          [1 ] Department of Chemistry, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States.
          [2 ] Institute of Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University , 40225 Düsseldorf, Germany.
          Article
          10.1021/ct300418h
          26605738
          2e6fcfbd-7f86-4067-b399-f3d516a19592
          History

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