Journal article
Current Status of the AMOEBA Polarizable Force Field
The journal of physical chemistry. B, Vol.114(8), pp.2549-2564
03/04/2010
DOI: 10.1021/jp910674d
PMCID: PMC2918242
PMID: 20136072
Abstract
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 towards 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 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 on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.
Details
- Title: Subtitle
- Current Status of the AMOEBA Polarizable Force Field
- Creators
- Jay W Ponder - Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO 63110Chuanjie Wu - Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO 63110Pengyu Ren - Department of Biomedical Engineering, University of Texas, Austin, Texas 78712-1062Vijay S Pande - Department of Chemistry, Stanford University, Stanford, CA 94305. Department of Computer Science, Stanford University, Stanford, CA 94305John D Chodera - Department of Chemistry, Stanford University, Stanford, CA 94305Michael J Schnieders - Department of Chemistry, Stanford University, Stanford, CA 94305Imran Haque - Department of Computer Science, Stanford University, Stanford, CA 94305David L Mobley - Department of Chemistry, University of New Orleans, New Orleans, LA 70148Daniel S Lambrecht - Department of Chemistry, University of California, Berkeley, CA 94720Robert A DiStasio - Department of Chemistry, University of California, Berkeley, CA 94720Martin Head-Gordon - Department of Chemistry, University of California, Berkeley, CA 94720Gary N. I Clark - Department of Bioengineering, University of California, Berkeley, CA 94720Margaret E Johnson - Department of Bioengineering, University of California, Berkeley, CA 94720Teresa Head-Gordon - Department of Bioengineering, University of California, Berkeley, CA 94720
- Resource Type
- Journal article
- Publication Details
- The journal of physical chemistry. B, Vol.114(8), pp.2549-2564
- DOI
- 10.1021/jp910674d
- PMID
- 20136072
- PMCID
- PMC2918242
- NLM abbreviation
- J Phys Chem B
- ISSN
- 1520-6106
- eISSN
- 1520-5207
- Publisher
- American Chemical Society
- Language
- English
- Date published
- 03/04/2010
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984024412902771
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