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

被引：3304

作者：

Miller, Bill R., III ^{[1
]}

McGee, T. Dwight, Jr. ^{[1
]}

Swails, Jason M. ^{[1
]}

Homeyer, Nadine ^{[2
]}

Gohlke, Holger ^{[2
]}

Roitberg, Adrian E. ^{[1
]}

机构：

[1] Univ Florida, Dept Chem, Quantum Theory Project, Gainesville, FL 32611 USA

[2] Univ Dusseldorf, Dept Math & Nat Sci, Inst Pharmaceut & Med Chem, D-40225 Dusseldorf, Germany

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2012年 / 8卷 / 09期

基金：

美国国家科学基金会;

关键词：

MOLECULAR-MECHANICS; CONTINUUM SOLVENT; BINDING; DOCKING; QM/MM; DNA;

D O I：

10.1021/ct300418h

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

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.

引用

页码：3314 / 3321

页数：8

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