title: The Amber biomolecular simulation programs.
abstract: We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA. case@scripps.edu
authors.forename: David A
authors.initials: DA
authors.lastname: Case
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
authors.forename: Tom
authors.initials: T
authors.lastname: Darden
authors.forename: Holger
authors.initials: H
authors.lastname: Gohlke
authors.forename: Ray
authors.initials: R
authors.lastname: Luo
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Merz
authors.forename: Alexey
authors.initials: A
authors.lastname: Onufriev
authors.forename: Carlos
authors.initials: C
authors.lastname: Simmerling
authors.forename: Bing
authors.initials: B
authors.lastname: Wang
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Woods
mesh_terms: D000465:Algorithms; D002241:Carbohydrates / Q000737:chemistry; D003198:Computer Simulation / Q000639:trends*; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D009696:Nucleic Acids / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D012984:Software / Q000639:trends*; D013816:Thermodynamics
chemical_list: D002241:Carbohydrates; D009696:Nucleic Acids; D011506:Proteins