Current Status of the AMOEBA Polarizable Force Field

被引:1060
作者
Ponder, Jay W. [2 ]
Wu, Chuanjie [2 ]
Ren, Pengyu [3 ]
Pande, Vijay S. [4 ,5 ]
Chodera, John D. [4 ,5 ]
Schnieders, Michael J. [4 ,5 ]
Haque, Imran [4 ,5 ]
Mobley, David L. [6 ]
Lambrecht, Daniel S. [7 ]
DiStasio, Robert A., Jr. [7 ]
Head-Gordon, Martin [7 ]
Clark, Gary N. I. [1 ]
Johnson, Margaret E. [1 ]
Head-Gordon, Teresa [1 ]
机构
[1] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA
[2] Washington Univ, Dept Biochem & Mol Biophys, St Louis, MO 63110 USA
[3] Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USA
[4] Stanford Univ, Dept Chem, Stanford, CA 94305 USA
[5] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA
[6] Univ New Orleans, Dept Chem, New Orleans, LA 70148 USA
[7] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA
基金
美国国家科学基金会;
关键词
BINDING FREE-ENERGIES; MOLECULAR-DYNAMICS SIMULATIONS; DISTRIBUTED MULTIPOLE ANALYSIS; PLESSET PERTURBATION-THEORY; HYDRATION WATER DYNAMICS; INITIO QUANTUM-CHEMISTRY; PARTICLE MESH EWALD; AB-INITIO; BIOMOLECULAR SIMULATIONS; CONDENSED-PHASE;
D O I
10.1021/jp910674d
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
Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule Structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially Successful oil protein-ligand binding and Computational X-ray crystallography where polarization and accurate electrostatics are critical.
引用
收藏
页码:2549 / 2564
页数:16
相关论文
共 103 条
[41]   Quantitative quantum chemistry [J].
Helgaker, Trygve ;
Klopper, Wim ;
Tew, David P. .
MOLECULAR PHYSICS, 2008, 106 (16-18) :2107-2143
[42]   GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation [J].
Hess, Berk ;
Kutzner, Carsten ;
van der Spoel, David ;
Lindahl, Erik .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2008, 4 (03) :435-447
[43]   Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew [J].
Horn, HW ;
Swope, WC ;
Pitera, JW ;
Madura, JD ;
Dick, TJ ;
Hura, GL ;
Head-Gordon, T .
JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (20) :9665-9678
[44]   Comparison of multiple amber force fields and development of improved protein backbone parameters [J].
Hornak, Viktor ;
Abel, Robert ;
Okur, Asim ;
Strockbine, Bentley ;
Roitberg, Adrian ;
Simmerling, Carlos .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2006, 65 (03) :712-725
[45]   Calculation of protein-ligand binding free energy by using a polarizable potential [J].
Jiao, Dian ;
Golubkov, Pavel A. ;
Darden, Thomas A. ;
Ren, Pengyu .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (17) :6290-6295
[46]   Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential [J].
Jiao, Dian ;
King, Christopher ;
Grossfield, Alan ;
Darden, Thomas A. ;
Ren, Pengyu .
JOURNAL OF PHYSICAL CHEMISTRY B, 2006, 110 (37) :18553-18559
[47]   Trypsin-Ligand Binding Free Energies from Explicit and Implicit Solvent Simulations with Polarizable Potential [J].
Jiao, Dian ;
Zhang, Jiajing ;
Duke, Robert E. ;
Li, Guohui ;
Schnieders, Michael J. ;
Ren, Pengyu .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (11) :1701-1711
[48]   Effects of co-solvents on peptide hydration water structure and dynamics [J].
Johnson, Margaret E. ;
Malardier-Jugroot, Cecile ;
Head-Gordon, Teresa .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2010, 12 (02) :393-405
[49]   Hydration Water Dynamics Near Biological Interfaces [J].
Johnson, Margaret E. ;
Malardier-Jugroot, Cecile ;
Murarka, Rajesh K. ;
Head-Gordon, Teresa .
JOURNAL OF PHYSICAL CHEMISTRY B, 2009, 113 (13) :4082-4092
[50]   Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids [J].
Jorgensen, WL ;
Maxwell, DS ;
TiradoRives, J .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, 118 (45) :11225-11236