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

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Department of Chemistry, Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
Institute of Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University, 40225 Düsseldorf, Germany
Cite this: J. Chem. Theory Comput. 2012, 8, 9, 3314–3321
Publication Date (Web):July 25, 2012
https://doi.org/10.1021/ct300418h
Copyright © 2012 American Chemical Society

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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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