title: MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
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.
authors.affiliation: Department of Chemistry, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States.
authors.forename: Bill R
authors.initials: BR
authors.lastname: Miller
authors.affiliation: Department of Chemistry, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States.
authors.forename: T Dwight
authors.initials: TD
authors.lastname: McGee
authors.affiliation: Department of Chemistry, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Swails
authors.affiliation: Institute of Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University , 40225 Düsseldorf, Germany.
authors.forename: Nadine
authors.initials: N
authors.lastname: Homeyer
authors.affiliation: Institute of Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University , 40225 Düsseldorf, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Gohlke
authors.affiliation: Department of Chemistry, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States.
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Roitberg