2005 December ; 26(16): 1668–1688 | DAVID A. CASE, THOMAS E. CHEATHAM III, TOM DAR DEN, HOLGER GOHLKE, RAY LUO, KENNETH M. MERZ JR., ALEXEY ONUFRIEV, CARLOS SIMMERLING, BING WANG, and ROBERT J. WOODS
The article provides an overview of the development, features, and future directions of the Amber package of computer programs, which are widely used for molecular dynamics simulations of proteins, nucleic acids, and carbohydrates. Amber consists of a suite of interconnected programs designed to work together, facilitating system preparation, simulation, and trajectory analysis. The main preparation programs, *antechamber* and *LeaP*, assemble force fields and construct biopolymers, respectively. The primary simulation program, *sander*, is a parallel Fortran 90 code that performs molecular dynamics simulations. The *ptraj* analysis program handles large trajectory files and provides various analysis tasks. Amber supports explicit and implicit solvent models, with the latter being more efficient for implicit solvent simulations. The article also discusses the strengths and weaknesses of Amber, including its limitations in handling vacuum simulations and nonbonded cutoffs. Additionally, it covers the development of force fields, particularly the GLYCAM force field for carbohydrates, and the QM/MM approach for studying enzyme reactions and protein-ligand interactions. The article concludes by addressing the treatment of solvent effects, including explicit solvent models and the particle-mesh Ewald (PME) method for long-range electrostatic interactions.The article provides an overview of the development, features, and future directions of the Amber package of computer programs, which are widely used for molecular dynamics simulations of proteins, nucleic acids, and carbohydrates. Amber consists of a suite of interconnected programs designed to work together, facilitating system preparation, simulation, and trajectory analysis. The main preparation programs, *antechamber* and *LeaP*, assemble force fields and construct biopolymers, respectively. The primary simulation program, *sander*, is a parallel Fortran 90 code that performs molecular dynamics simulations. The *ptraj* analysis program handles large trajectory files and provides various analysis tasks. Amber supports explicit and implicit solvent models, with the latter being more efficient for implicit solvent simulations. The article also discusses the strengths and weaknesses of Amber, including its limitations in handling vacuum simulations and nonbonded cutoffs. Additionally, it covers the development of force fields, particularly the GLYCAM force field for carbohydrates, and the QM/MM approach for studying enzyme reactions and protein-ligand interactions. The article concludes by addressing the treatment of solvent effects, including explicit solvent models and the particle-mesh Ewald (PME) method for long-range electrostatic interactions.