Journal of Chemical Theory and Computation· 2012Q1
<i>MMPBSA.py</i>: An Efficient Program for End-State Free Energy Calculations
- 4,537citations
- Q1SCImago
- 2012year
Short summary
MMPBSA.py is a new Python program that streamlines end-state free energy calculations for molecules in solution, offering multiple solvation models and parallel processing for speed.
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Key points
- MMPBSA.py automates free energy calculations from MD/MC simulations.
- Includes Poisson-Boltzmann, Generalized Born, and Reference Interaction Site Model solvation.
- Supports entropy approximation via normal mode or quasi-harmonic analysis.
- Parallel processing significantly speeds up computation time.
- Offers free energy decomposition and alanine scanning for specific interaction analysis.
AI-generated from the title and abstract; the full text is not read.
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.
The authors' abstract, as published at the source. Journal of Chemical Theory and Computation, 2012 · DOI ↗
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Field: Atomic and Molecular Physics, and Optics
Atomic and Molecular Physics, and OpticsPhysics and Astronomy