AMBER A Program for Simulation of Biological and Organic Molecules

AMBER A Program for Simulation of Biological and Organic Molecules 

Peter Kollman, James W. Caldwell, and Wilson S. Ross 

Smith Kline Beecham Pharmaceuticals, King of Prussia, PA, USA 

AMBER is a set of computer programs that use molecular mechanics, molecular dynamics, normal mode analysis, and free energy calculations to simulate accurately the properties of complex molecules and their interactions, both in vacuo and in condensed phases. A detailed description of the history and current form of AMBER has recently been published, so this article will attempt to give an overview of the program and the features which distinguish it from related programs. 

The development of AMBER has been motivated mainly by applications to molecules of biological interest. In the period 1979-85, this corresponded mainly to applications of molecular mechanics, but in the ensuing decade, applications have increasingly involved molecular dynamics with explicit representation of solvent. Nonetheless, molecular mechanics remains an essential feature of the evaluation of force field parameters, which govern how accurately the properties of a system can be simulated. These parameters are  

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Kollman P et al (1998) AMBER a program for simulation of biological and organic molecules. In Schleyer PV et al (eds) Encyclopedia of computational chemistry. Wiley, Chichester... 

AMBER A PROGRAM FOR SIMULATION OF BIOLOGICAL AND ORGANIC MOLECULES 11... 

AMBER A Program for Simulation of Biological and Organic Molecules Atoms in Molecules Charge Flux Electronic Wavefunctions Analysis Electrostatic Potentials Chemical Applications Free Energy Changes in Solution Natural Bond Orbital Methods Natural Orbitals. 

AMI AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Divide and Conquer for Semiempirical MO Methods Electrostatic Catalysis Force Fields A General Discussion Force Fields CFF GROMOS Force Field Hybrid Methods Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Methods Mixed Quantum-Classical Methods MNDO MNDO/d Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Parameterization of Semiempirical MO Methods PM3 Protein Force Fields Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM) SINDOI Parameterization and Application. 

AMBER A Program for Simulation of Biological and Organic Molecules Anharmonic Molecular Force Fields ... 

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