Journal of Computational ChemistryVolume 26, Issue 16 p. 1668-1688 The Amber biomolecular simulation programs David A. Case, Corresponding Author David A. Case [email protected] Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037Search for more papers by this authorThomas E. Cheatham III, Thomas E. Cheatham III Departments of Medicinal Chemistry, Pharmaceutics & Pharmaceutical Chemistry, and Bioengineering, 2000 East, 30 South, Skaggs Hall 201, University of Utah, Salt Lake City, Utah 84112Search for more papers by this authorTom Darden, Tom Darden National Institute of Environmental Health Sciences, Laboratory of Structural Biology, Mail Drop F3-02, PO Box 12233 Research Triangle Park, North Carolina 27709Search for more papers by this authorHolger Gohlke, Holger Gohlke Fachbereich Biologie und Informatik, J.W. Goethe-Universität, Marie-Curie-Str. 9, 60439 Frankfurt/Main, GermanySearch for more papers by this authorRay Luo, Ray Luo Department of Molecular Biology and Biochemistry, University of California, 5.3206 Natural Science I, Irvine, California 92697Search for more papers by this authorKenneth M. Merz Jr., Kenneth M. Merz Jr. Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802Search for more papers by this authorAlexey Onufriev, Alexey Onufriev Department of Computer Science, Virgina Tech, 600 McBryde (MC 0106) Blacksburg, Virginia 24061Search for more papers by this authorCarlos Simmerling, Carlos Simmerling Department of Chemistry, Stony Brook University, Stony Brook, New York 11794Search for more papers by this authorBing Wang, Bing Wang Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037Search for more papers by this authorRobert J. Woods, Robert J. Woods Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, Georgia 30602Search for more papers by this author David A. Case, Corresponding Author David A. Case [email protected] Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037Search for more papers by this authorThomas E. Cheatham III, Thomas E. Cheatham III Departments of Medicinal Chemistry, Pharmaceutics & Pharmaceutical Chemistry, and Bioengineering, 2000 East, 30 South, Skaggs Hall 201, University of Utah, Salt Lake City, Utah 84112Search for more papers by this authorTom Darden, Tom Darden National Institute of Environmental Health Sciences, Laboratory of Structural Biology, Mail Drop F3-02, PO Box 12233 Research Triangle Park, North Carolina 27709Search for more papers by this authorHolger Gohlke, Holger Gohlke Fachbereich Biologie und Informatik, J.W. Goethe-Universität, Marie-Curie-Str. 9, 60439 Frankfurt/Main, GermanySearch for more papers by this authorRay Luo, Ray Luo Department of Molecular Biology and Biochemistry, University of California, 5.3206 Natural Science I, Irvine, California 92697Search for more papers by this authorKenneth M. Merz Jr., Kenneth M. Merz Jr. Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802Search for more papers by this authorAlexey Onufriev, Alexey Onufriev Department of Computer Science, Virgina Tech, 600 McBryde (MC 0106) Blacksburg, Virginia 24061Search for more papers by this authorCarlos Simmerling, Carlos Simmerling Department of Chemistry, Stony Brook University, Stony Brook, New York 11794Search for more papers by this authorBing Wang, Bing Wang Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037Search for more papers by this authorRobert J. Woods, Robert J. Woods Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, Georgia 30602Search for more papers by this author First published: 30 September 2005 https://doi.org/10.1002/jcc.20290Citations: 6,634Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat 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. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1668–1688, 2005 References 1 Weiner, P.; Kollman, P. J Comput Chem 1981, 2, 287. 2 Pearlman, D.; Case, D.; Caldwell, J.; Ross, W.; Cheatham, T., III; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comp Phys Commun 1995, 91, 1. 3 Allen, M.; Tildesley, D. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987. 4 Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications; Academic Press: San Diego, 1996. 5 Becker, O.; MacKerell, A.; Roux, B.; Watanabe, M. Computational Biochemistry and Biophysics; Marcel Dekker: New York, 2001. 6 Cramer, C. Essentials of Computational Chemistry: Theories and Models; John Wiley & Sons: New York, 2002. 7 Schlick, T. Molecular Modeling and Simulation; Springer-Verlag: New York, 2002. 8 Kalé, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J Comput Phys 1999, 151, 283. 9 Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graphics 1996, 14, 33. 10 Feig, M.; Karanicolas, J. L.; Brooks, C. L., III. J Mol Graph Model 2004, 22, 377. 11 Macke, T.; Case, D. In Molecular Modeling of Nucleic Acids; N. Leontis; J. Santa Lucia, Eds.; American Chemical Society: Washington, DC, 1998, p. 379. 12 Crowley, M.; Darden, T.; Cheatham, T., III; Deerfield, D., II. J Supercomput 1997, 11, 255. 13 Srinivasan, J.; Cheatham, T. E., III; Kollman, P.; Case, D. J Am Chem Soc 1998, 120, 9401. 14 Kollman, P.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D.; Cheatham, T. E., III. Acc Chem Res 2000, 33, 889. 15 Gohlke, H.; Case, D. J Comput Chem 2004, 25, 238. 16 Weiner, S.; Kollman, P.; Case, D.; Singh, U.; Ghio, C.; Alagona, G.; Profeta, Jr., S.; Weiner, P. J Am Chem Soc 1984, 106, 765. 17 Cornell, W.; Cieplak, P.; Bayly, C.; Gould, I.; Merz, K., Jr.; Ferguson, D.; Spellmeyer, D.; Fox, T.; Caldwell, J.; Kollman, P. J Am Chem Soc 1995, 117, 5179. 18 García, A.; Sanbonmatsu, K. Proc Natl Acad Sci USA 2002, 99, 2782. 19 Simmerling, C.; Strockbine, B.; Roitberg, A. J. Am Chem Soc 2002, 124, 11258. 20 Okur, A.; Strockbine, B.; Hornak, V.; Simmerling, C. J Comput Chem 2003, 24, 21. 21 Ponder, J.; Case, D. Adv Protein Chem 2003, 66, 27. 22 Cheatham, T. E., III; Young, M. Biopolymers (Nucleic Acid Sci) 2001, 56, 232. 23 Wang, J.; Wolf, R.; Caldwell, J.; Kollman, P.; Case, D. J Comput Chem 2004, 25, 1157. 24 Rick, S.; Stuart, S. Rev Comput Chem 2002, 18, 89. 25 Grossfield, A.; Ren, P.; Ponder, J. J Am Chem Soc 2003, 125, 15671. 26 Kaminski, G.; Stern, H.; Berne, B.; Friesner, R. J Phys Chem A 2004, 108, 621. 27 Mannfors, B.; Mirkin, N.; Palmo, K.; Krimm, S. J Phys Chem A 2003, 107, 1825. 28 Woods, R. J Phys Chem 1995, 99, 3832. 29 Basma, M. J Comput Chem 2000, 22, 1125. 30 Woods, R.; Chappelle, R. J Mol Struct 2000, 527, 149. 31 Wolfe, S.; Whangbo, M.-H.; Mitchell, D. Carbohydr Res 1979, 69, 1. 32 Wolfe, S. Acc Chem Res 1972, 5, 102. 33 Marchessault, R.; Perez, S. Biopolymers 1979, 18, 2369. 34 Nishida, Y.; Ohrui, H.; Meguro, H. Tetrahedron Lett 1984, 25, 1575. 35 Kroon–Batenburg, L.; Krron, J. Biopolymers 1990, 29, 1243. 36 Tvaroska, I.; Carver, J. J Phys Chem B 1997, 101, 2992. 37 Kirschner, K.; Woods, R. Proc Natl Acad Sci USA 2001, 98, 10541. 38 Warshel, A.; Levitt, M. J Mol Biol 1976, 103, 227. 39 Singh, U.; Kollman, P. J Comput Chem 1986, 7, 718. 40 Gao, J. Rev Comput Chem 1995, 7, 119. 41 Monard, G.; Merz, K. Acc Chem Res 1999, 32, 904. 42 Ryde, U. Curr Opin Chem Biol 2003, 7, 136. 43 Dixon, S.; Merz, K. J Chem Phys 1996, 104, 6643. 44 Dixon, S.; Merz, K. J Chem Phys 1997, 107, 879. 45 Yang, W.; Lee, T. J Chem Phys 1995, 103, 5674. 46 van der Vaart, A.; Gogonea, V.; Merz, K., Jr. J Comput Chem 2000, 21, 1494. 47 Théry, V.; Rinaldi, D.; Rivail, J.; Maigret, B.; Ferenczy, G. J Comput Chem 1994, 15, 269. 48 Gao, J.; Amara, P.; Field, M. J Phys Chem A 1998, 102, 4714. 49 Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. J Phys Chem A 2000, 104, 1720. 50 Wang, B.; Raha, K.; Merz, K. J Am Chem Soc 2004, 126, 11430. 51 Jorgensen, W. J Chem Phys 1982, 77, 4156. 52 Jorgensen, W.; Chandrasekhar, J.; Madura, J.; Klein, M. J Chem Phys 1983, 79, 926. 53 Jorgensen, W.; Madura, J. Mol Phys 1985, 56, 1381. 54 Horn, H.; Swope, W.; Pitera, J.; Madura, J.; Dick, T.; Hura, G.; Head–Gordon, T. J Chem Phys 2004, 120, 9665. 55 Mahoney, M.; Jorgensen, W. J Chem Phys 2000, 112, 8910. 56 Berendsen, H.; Grigera, J.; Straatsma, T. J Phys Chem 1987, 91, 6269. 57 Caldwell, J.; Kollman, P. J Phys Chem 1995, 99, 6208. 58 Hockney, R.; Eastwood, J. Computer Simulation Using Particles; McGraw–Hill: New York, 1981. 59 Ewald, P. Ann Phys 1921, 64, 253. 60 DeLeeuw, S.; Perram, J.; Smith, E. Annu Rev Phys Chem 1986, 37, 245. 61 Kittel, C. Introduction to Solid State Physics; John Wiley & Sons: New York, 1986. 62 Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089. 63 Essmann, U.; Perera, L.; Berkowitz, M.; Darden, T.; Lee, H.; Pedersen, L. J Chem Phys 1995, 103, 8577. 64 Pollock, E.; Glosli, J. Comp Phys Commun 1996, 95, 93. 65 Sagui, C.; Darden, T. In Simulation and Theory of Electrostatic Interactions in Solution; L. Pratt; G. Hummer, Eds.; American Institute of Physics: Melville, NY, 1999, p. 104. 66 Hummer, G.; Pratt, L.; García, A. J Phys Chem 1996, 100, 1206. 67 Hünenberger, P.; McCammon, J. Biophys Chem 1999, 78, 69. 68 Kastenholz, M.; Hunenberger, P. J Phys Chem B 2004, 108, 774. 69 Feller, S.; Pastor, R.; Rojnuckarin, A.; Bogusz, S.; Brooks, B. J Phys Chem 1996, 100, 17011. 70 Patra, M.; Karttunen, M.; T. Hyvonen, M.; Falck, E. J Phys Chem B 2004, 108, 4485. 71 Dixon, R.; Kollman, P. J Comput Chem 1997, 18, 1632. 72 Cieplak, P.; Caldwell, J.; Kollman, P. J Comput Chem 2001, 22, 1048. 73 Smith, W. CCP5 Inform Q 1982, 4. 74 Toukmaji, A.; Sagui, C.; Board, J.; Darden, T. J Chem Phys 2000, 113, 10913. 75 Ren, P.; Ponder, J. J Phys Chem B 2003, 107, 5933. 76 Thole, B. Chem Phys 1981, 59, 341. 77 Sagui, C.; Pedersen, L.; Darden, T. J Chem Phys 2004, 120, 73. 78 McMurchie, L.; Davidson, E. J Comput Phys 1978, 26, 218. 79 Grossfield, A.; Ren, P.; Ponder, J. W. J Am Chem Soc 2003, 125, 15671. 80 Baucom, J.; Transue, T.; Fuentes–Cabrera, M.; Krahn, J.; Darden, T.; Sagui, C. J Chem Phys 2004, 121, 6998. 81 Cramer, C.; Truhlar, D. Chem Rev 1999, 99, 2161. 82 Bashford, D.; Case, D. Annu Rev Phys Chem 2000, 51, 129. 83 Feig, M.; Brooks, C. L., III. Curr Opin Struct Biol 2004, 14, 217. 84 Sitkoff, D.; Sharp, K.; Honig, B. J Phys Chem 1994, 98, 1978. 85 Simonson, T. Rep Prog Phys 2003, 66, 737. 86 Levy, R.; Zhang, L.; Gallicchio, E.; Felts, A. J Am Chem Soc 2003, 125, 9523. 87 Gallicchio, E.; Levy, R. J Comput Chem 2004, 25, 479. 88 Weiser, J.; Shenkin, P.; Still, W. J Comput Chem 1999, 20, 217. 89 Baker, N. Methods Enzymol 2004, 383, 94. 90 Honig, B.; Sharp, K.; Yang, A.-S. J Phys Chem 1993, 97, 1101. 91 Honig, B.; Nicholls, A. Science 1995, 268, 1144. 92 Luo, R.; David, L.; Gilson, M. J Comput Chem 2002, 23, 1244. 93 Davis, M.; McCammon, J. J Comput Chem 1991, 12, 909. 94 Gilson, M.; Sharp, K.; Honig, B. J Comp Chem 1988, 9, 327. 95 Lu, Q.; Luo, R. J Chem Phys 2003, 119, 11035. 96 Feig, M.; Im, W.; Brooks, C. J Chem Phys 2004, 120, 903. 97 Still, W.; Tempczyk, A.; Hawley, R.; Hendrickson, T. J Am Chem Soc 1990, 112, 6127. 98 Jayaram, B.; Liu, Y.; Beveridge, D. J Phys Chem 1998, 109, 1465. 99 Onufriev, A.; Case, D.; Bashford, D. J Comput Chem 2002, 23, 1297. 100 Sigalov, G.; Scheffe, P.; Onufriev, A. J Chem Phys 2005, 122, 094511. 101 Onufriev, A.; Bashford, D.; Case, D. J Phys Chem B 2000, 104, 3712. 102 Hawkins, G.; Cramer, C.; Truhlar, D. Chem Phys Lett 1995, 246, 122. 103 Hawkins, G.; Cramer, C.; Truhlar, D. J Phys Chem 1996, 100, 19824. 104 Srinivasan, J.; Trevathan, M.; Beroza, P.; Case, D. Theor Chem Acc 1999, 101, 426. 105 Bondi, A. J Chem Phys 1964, 64, 441. 106 Feig, M.; Onufriev, A.; Lee, M.; Im, W.; Case, D.; Brooks, C. L., III. J Comput Chem 2004, 25, 265. 107 Schaefer, M.; Froemmel, C. J Mol Biol 1990, 216, 1045. 108 Schaefer, M.; Karplus, M. J Phys Chem 1996, 100, 1578. 109 Onufriev, A.; Bashford, D.; Case, D. Proteins 2004, 55, 383. 110Roitberg, A.; Simmerling, C., Eds. J Mol Graph Model 2004, 22, 317. 111 Elber, R.; Karplus, M. J Am Chem Soc 1990, 112, 9161. 112 Roitberg, A.; Elber, R. J Chem Phys 1991, 95, 9277. 113 Hornak, V.; Simmerling, C. Proteins 2003, 51, 577. 114 Simmerling, C.; Miller, J.; Kollman, P. J Am Chem Soc 1998, 120, 7149. 115 Simmerling, C.; Lee, M.; Ortiz, A.; Kolinski, A.; Skolnick, J.; Kollman, P. J Am Chem Soc 2000, 122, 8392. 116 Cheng, X.; Hornak, V.; Simmerling, C. J Phys Chem B 2004, 108, 426. 117 Kirkpatrick, S.; Gelatt, C., Jr.; Vecchi, M. Science 1983, 220, 671. 118 Sugita, Y.; Okamoto, Y. Chem Phys Lett 1999, 314, 141. 119 Sugita, Y.; Okamoto, Y. Prog Theor Phys Suppl 2000, 138, 402. 120 Sugita, Y.; Kitao, A.; Okamoto, Y. J Chem Phys 2000, 113, 6042. 121 Mitsutake, A.; Sugita, Y.; Okamoto, Y. Biopolymers 2001, 60, 96. 122 Rhee, Y.; Pande, V. Biophys J 2003, 84, 775. 123 Pitera, J.; Swope, W. Proc Natl Acad Sci USA 2003, 100, 7587. 124 Karanicolas, J.; Brooks, C. Proc Natl Acad Sci USA 2003, 100, 3954. 125 Nymeyer, H.; Garcia, A.; Woolf, T. Biophys J. 2003, 84, 381A. 126 Kinnear, B.; Jarrold, M.; Hansmann, U. J Mol Graph Model 2004, 22, 397. 127 Ferrin, T.; Huang, C.; Jarvis, L.; Langridge, R. J Mol Graph 1988, 6, 13, 36. 128 Gohlke, H.; Kiel, C.; Case, D. J Mol Biol 2003, 330, 891. 129 Ichiye, T.; Karplus, M. Proteins Struct Funct Genet 1991, 11, 205. 130 Hünenberger, P.; Mark, A.; van Gunsteren, W. J Mol Biol 1995, 252, 492. 131 Hayward, S.; Go, N. Annu Rev Phys Chem 1995, 46, 223. 132 Karplus, M.; Kushick, J. Macromolecules 1981, 14, 325. 133 Levy, R.; Karplus, M.; Kushick, J.; Perahia, D. Macromolecules 1984, 17, 1370. 134 Abseher, R.; Nilges, M. J Mol Biol 1998, 279, 911. 135 Prompers, J.; Brüschweiler, R. Proteins 2002, 46, 177. 136 Amadei, A.; Linssen, A.; Berendsen, H. Proteins 1993, 17, 412. 137 Schäfer, H.; Mark, A.; van Gunsteren, W. J Chem Phys 2000, 113, 7809. 138 Schafer, H.; Daura, X.; van Gunsteren, W. Proteins 2001, 43, 45. 139 Smith, P.; van Gunsteren, W. J Mol Biol 1994, 236, 629. 140 Lipari, G.; Szabo, A. J Am Chem Soc 1982, 104, 4546. 141 Levy, R.; Karplus, M.; Wolynes, P. J Am Chem Soc 1981, 103, 5998. 142 Palmer, A.; Case, D. J Am Chem Soc 1992, 114, 9059. 143 Peter, C.; Daura, X.; vanGunsteren, W. J Biomol NMR 2001, 20, 297. 144 Prompers, J.; Brüschweiler, R. J Am Chem Soc 2001, 123, 7305. 145 Prompers, J.; Brüschweiler, R. J Am Chem Soc 2002, 124, 4522. Citing Literature Volume26, Issue16December 2005Pages 1668-1688 ReferencesRelatedInformation