共 103 条
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.
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页码:2549 / 2564
页数:16
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