The Amber Biomolecular Simulation Programs

David Case

Thomas Cheatham

Tom Darden

Holger Gohlke

^{Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037}

^{Departments of Medicinal Chemistry, Pharmaceutics & Pharmaceutical Chemistry, and Bioengineering, 2000 East, 30 South, Skaggs Hall 201, University of Utah, Salt Lake City, Utah 84112}

^{National Institute of Environmental Health Sciences, Laboratory of Structural Biology, Mail Drop F3-02, PO Box 12233 Research Triangle Park, North Carolina 27709}

^{Fachbereich Biologie und Informatik, J.W. Goethe-Universität, Marie-Curie-Str. 9, 60439 Frankfurt/Main, Germany}

^{Department of Molecular Biology and Biochemistry, University of California, 5.3206 Natural Science I, Irvine, California 92697}

^{Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802}

^{Department of Computer Science, Virgina Tech, 600 McBryde (MC 0106) Blacksburg, Virginia 24061}

^{Department of Chemistry, Stony Brook University, Stony Brook, New York 11794}

^{Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, Georgia 30602}

Correspondence to: D. A. Case; e-mail:ude.sppircs@esac

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.

Keywords: Amber, biomolecular simulation programs

Abstract

References

1. Weiner P, Kollman P. J Comput Chem. 1981;2:287.[PubMed]
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.[PubMed]
3. Allen, M.; Tildesley, DComputer Simulation of Liquids; Clarendon Press: Oxford, 1987.
4. Frenkel, D.; Smit, BUnderstanding Molecular Simulation: From Algorithms to Applications; Academic Press: San Diego, 1996.
5. Becker, O.; MacKerell, A.; Roux, B.; Watanabe, MComputational Biochemistry and Biophysics; Marcel Dekker: New York, 2001.
6. Cramer, CEssentials of Computational Chemistry: Theories and Models; John Wiley & Sons: New York, 2002.
7. Schlick, TMolecular 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.[PubMed]
9. Humphrey W, Dalke A, Schulten K. J Mol Graphics. 1996;14:33.[PubMed]
10. Feig M, Karanicolas JL, Brooks CL., III J Mol Graph Model. 2004;22:377.[PubMed]
11. Macke, T.; Case, D. In Molecular Modeling of Nucleic Acids; Leontis, N.; Santa Lucia, J., 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.[PubMed]
13. Srinivasan J, Cheatham TE, III, Kollman P, Case D. J Am Chem Soc. 1998;120:9401.[PubMed]
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 TE., III Acc Chem Res. 2000;33:889.[PubMed]
15. Gohlke H, Case D. J Comput Chem. 2004;25:238.[PubMed]
16. Weiner S, Kollman P, Case D, Singh U, Ghio C, Alagona G, Profeta S, Jr, Weiner P. J Am Chem Soc. 1984;106:765.[PubMed]
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.[PubMed]
18. García A, Sanbonmatsu K. Proc Natl Acad Sci USA. 2002;99:2782.
19. Simmerling C, Strockbine B, Roitberg AJ. Am Chem Soc. 2002;124:11258.[PubMed]
20. Okur A, Strockbine B, Hornak V, Simmerling C. J Comput Chem. 2003;24:21.[PubMed]
21. Ponder J, Case D. Adv Protein Chem. 2003;66:27.[PubMed]
22. Cheatham TE, III, Young M. Biopolymers (Nucleic Acid Sci) 2001;56:232.[PubMed]
23. Wang J, Wolf R, Caldwell J, Kollman P, Case D. J Comput Chem. 2004;25:1157.[PubMed]
24. Rick S, Stuart S. Rev Comput Chem. 2002;18:89.[PubMed]
25. Grossfield A, Ren P, Ponder J. J Am Chem Soc. 2003;125:15671.[PubMed]
26. Kaminski G, Stern H, Berne B, Friesner R. J Phys Chem A. 2004;108:621.[PubMed]
27. Mannfors B, Mirkin N, Palmo K, Krimm S. J Phys Chem A. 2003;107:1825.[PubMed]
28. Woods R. J Phys Chem. 1995;99:3832.[PubMed]
29. Basma M. J Comput Chem. 2000;22:1125.
30. Woods R, Chappelle R. J Mol Struct. 2000;527:149.
31. Wolfe S, Whangbo MH, Mitchell D. Carbohydr Res. 1979;69:1.[PubMed]
32. Wolfe S. Acc Chem Res. 1972;5:102.[PubMed]
33. Marchessault R, Perez S. Biopolymers. 1979;18:2369.[PubMed]
34. Nishida Y, Ohrui H, Meguro H. Tetrahedron Lett. 1984;25:1575.[PubMed]
35. Kroon–Batenburg L, Krron J. Biopolymers. 1990;29:1243.[PubMed]
36. Tvaroska I, Carver J. J Phys Chem B. 1997;101:2992.[PubMed]
37. Kirschner K, Woods R. Proc Natl Acad Sci USA. 2001;98:10541.
38. Warshel A, Levitt M. J Mol Biol. 1976;103:227.[PubMed]
39. Singh U, Kollman P. J Comput Chem. 1986;7:718.[PubMed]
40. Gao J. Rev Comput Chem. 1995;7:119.[PubMed]
41. Monard G, Merz K. Acc Chem Res. 1999;32:904.[PubMed]
42. Ryde U. Curr Opin Chem Biol. 2003;7:136.[PubMed]
43. Dixon S, Merz K. J Chem Phys. 1996;104:6643.[PubMed]
44. Dixon S, Merz K. J Chem Phys. 1997;107:879.[PubMed]
45. Yang W, Lee T. J Chem Phys. 1995;103:5674.[PubMed]
46. van der Vaart A, Gogonea V, Merz K., Jr J Comput Chem. 2000;21:1494.[PubMed]
47. Théry V, Rinaldi D, Rivail J, Maigret B, Ferenczy G. J Comput Chem. 1994;15:269.[PubMed]
48. Gao J, Amara P, Field M. J Phys Chem A. 1998;102:4714.[PubMed]
49. Reuter N, Dejaegere A, Maigret B, Karplus M. J Phys Chem A. 2000;104:1720.[PubMed]
50. Wang B, Raha K, Merz K. J Am Chem Soc. 2004;126:11430.[PubMed]
51. Jorgensen W. J Chem Phys. 1982;77:4156.[PubMed]
52. Jorgensen W, Chandrasekhar J, Madura J, Klein M. J Chem Phys. 1983;79:926.[PubMed]
53. Jorgensen W, Madura J. Mol Phys. 1985;56:1381.[PubMed]
54. Horn H, Swope W, Pitera J, Madura J, Dick T, Hura G, Head–Gordon T. J Chem Phys. 2004;120:9665.[PubMed]
55. Mahoney M, Jorgensen W. J Chem Phys. 2000;112:8910.[PubMed]
56. Berendsen H, Grigera J, Straatsma T. J Phys Chem. 1987;91:6269.[PubMed]
57. Caldwell J, Kollman P. J Phys Chem. 1995;99:6208.[PubMed]
58. Hockney, R.; Eastwood, JComputer Simulation Using Particles; McGraw–Hill: New York, 1981.
59. Ewald P. Ann Phys. 1921;64:253.[PubMed]
60. DeLeeuw S, Perram J, Smith E. Annu Rev Phys Chem. 1986;37:245.[PubMed]
61. Kittel, CIntroduction to Solid State Physics; John Wiley & Sons: New York, 1986.
62. Darden T, York D, Pedersen L. J Chem Phys. 1993;98:10089.[PubMed]
63. Essmann U, Perera L, Berkowitz M, Darden T, Lee H, Pedersen L. J Chem Phys. 1995;103:8577.[PubMed]
64. Pollock E, Glosli J. Comp Phys Commun. 1996;95:93.[PubMed]
65. Sagui, C.; Darden, T. In Simulation and Theory of Electrostatic Interactions in Solution; Pratt, L.; Hummer, G., Eds.; American Institute of Physics: Melville, NY, 1999, p. 104.
66. Hummer G, Pratt L, García A. J Phys Chem. 1996;100:1206.[PubMed]
67. Hünenberger P, McCammon J. Biophys Chem. 1999;78:69.[PubMed]
68. Kastenholz M, Hunenberger P. J Phys Chem B. 2004;108:774.[PubMed]
69. Feller S, Pastor R, Rojnuckarin A, Bogusz S, Brooks B. J Phys Chem. 1996;100:17011.[PubMed]
70. Patra M, Karttunen MT, Hyvonen M, Falck E. J Phys Chem B. 2004;108:4485.[PubMed]
71. Dixon R, Kollman P. J Comput Chem. 1997;18:1632.[PubMed]
72. Cieplak P, Caldwell J, Kollman P. J Comput Chem. 2001;22:1048.[PubMed]
73. Smith W. CCP5 Inform Q. 1982:4.[PubMed]
74. Toukmaji A, Sagui C, Board J, Darden T. J Chem Phys. 2000;113:10913.[PubMed]
75. Ren P, Ponder J. J Phys Chem B. 2003;107:5933.[PubMed]
76. Thole B. Chem Phys. 1981;59:341.[PubMed]
77. Sagui C, Pedersen L, Darden T. J Chem Phys. 2004;120:73.[PubMed]
78. McMurchie L, Davidson E. J Comput Phys. 1978;26:218.[PubMed]
79. Grossfield A, Ren P, Ponder JW. J Am Chem Soc. 2003;125:15671.[PubMed]
80. Baucom J, Transue T, Fuentes–Cabrera M, Krahn J, Darden T, Sagui C. J Chem Phys. 2004;121:6998.[PubMed]
81. Cramer C, Truhlar D. Chem Rev. 1999;99:2161.[PubMed]
82. Bashford D, Case D. Annu Rev Phys Chem. 2000;51:129.[PubMed]
83. Feig M, Brooks CL., III Curr Opin Struct Biol. 2004;14:217.[PubMed]
84. Sitkoff D, Sharp K, Honig B. J Phys Chem. 1994;98:1978.[PubMed]
85. Simonson T. Rep Prog Phys. 2003;66:737.[PubMed]
86. Levy R, Zhang L, Gallicchio E, Felts A. J Am Chem Soc. 2003;125:9523.[PubMed]
87. Gallicchio E, Levy R. J Comput Chem. 2004;25:479.[PubMed]
88. Weiser J, Shenkin P, Still W. J Comput Chem. 1999;20:217.[PubMed]
89. Baker N. Methods Enzymol. 2004;383:94.[PubMed]
90. Honig B, Sharp K, Yang AS. J Phys Chem. 1993;97:1101.[PubMed]
91. Honig B, Nicholls A. Science. 1995;268:1144.[PubMed]
92. Luo R, David L, Gilson M. J Comput Chem. 2002;23:1244.[PubMed]
93. Davis M, McCammon J. J Comput Chem. 1991;12:909.[PubMed]
94. Gilson M, Sharp K, Honig B. J Comp Chem. 1988;9:327.[PubMed]
95. Lu Q, Luo R. J Chem Phys. 2003;119:11035.[PubMed]
96. Feig M, Im W, Brooks C. J Chem Phys. 2004;120:903.[PubMed]
97. Still W, Tempczyk A, Hawley R, Hendrickson T. J Am Chem Soc. 1990;112:6127.[PubMed]
98. Jayaram B, Liu Y, Beveridge D. J Phys Chem. 1998;109:1465.[PubMed]
99. Onufriev A, Case D, Bashford D. J Comput Chem. 2002;23:1297.[PubMed]
100. Sigalov G, Scheffe P, Onufriev A. J Chem Phys. 2005;122:094511.[PubMed]
101. Onufriev A, Bashford D, Case D. J Phys Chem B. 2000;104:3712.[PubMed]
102. Hawkins G, Cramer C, Truhlar D. Chem Phys Lett. 1995;246:122.[PubMed]
103. Hawkins G, Cramer C, Truhlar D. J Phys Chem. 1996;100:19824.[PubMed]
104. Srinivasan J, Trevathan M, Beroza P, Case D. Theor Chem Acc. 1999;101:426.[PubMed]
105. Bondi A. J Chem Phys. 1964;64:441.[PubMed]
106. Feig M, Onufriev A, Lee M, Im W, Case D, Brooks CL., III J Comput Chem. 2004;25:265.[PubMed]
107. Schaefer M, Froemmel C. J Mol Biol. 1990;216:1045.[PubMed]
108. Schaefer M, Karplus M. J Phys Chem. 1996;100:1578.[PubMed]
109. Onufriev A, Bashford D, Case D. Proteins. 2004;55:383.[PubMed]
110. Roitberg A, Simmerling C. Eds J Mol Graph Model. 2004;22:317.[PubMed]
111. Elber R, Karplus M. J Am Chem Soc. 1990;112:9161.[PubMed]
112. Roitberg A, Elber R. J Chem Phys. 1991;95:9277.[PubMed]
113. Hornak V, Simmerling C. Proteins. 2003;51:577.[PubMed]
114. Simmerling C, Miller J, Kollman P. J Am Chem Soc. 1998;120:7149.[PubMed]
115. Simmerling C, Lee M, Ortiz A, Kolinski A, Skolnick J, Kollman P. J Am Chem Soc. 2000;122:8392.[PubMed]
116. Cheng X, Hornak V, Simmerling C. J Phys Chem B. 2004;108:426.[PubMed]
117. Kirkpatrick S, Gelatt C, Jr, Vecchi M. Science. 1983;220:671.[PubMed]
118. Sugita Y, Okamoto Y. Chem Phys Lett. 1999;314:141.[PubMed]
119. Sugita Y, Okamoto Y. Prog Theor Phys Suppl. 2000;138:402.[PubMed]
120. Sugita Y, Kitao A, Okamoto Y. J Chem Phys. 2000;113:6042.[PubMed]
121. Mitsutake A, Sugita Y, Okamoto Y. Biopolymers. 2001;60:96.[PubMed]
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.[PubMed]
126. Kinnear B, Jarrold M, Hansmann U. J Mol Graph Model. 2004;22:397.[PubMed]
127. Ferrin T, Huang C, Jarvis L, Langridge R. J Mol Graph 1988. 6;13:36.[PubMed]
128. Gohlke H, Kiel C, Case D. J Mol Biol. 2003;330:891.[PubMed]
129. Ichiye T, Karplus M. Proteins Struct Funct Genet. 1991;11:205.[PubMed]
130. Hünenberger P, Mark A, van Gunsteren W. J Mol Biol. 1995;252:492.[PubMed]
131. Hayward S, Go N. Annu Rev Phys Chem. 1995;46:223.[PubMed]
132. Karplus M, Kushick J. Macromolecules. 1981;14:325.[PubMed]
133. Levy R, Karplus M, Kushick J, Perahia D. Macromolecules. 1984;17:1370.[PubMed]
134. Abseher R, Nilges M. J Mol Biol. 1998;279:911.[PubMed]
135. Prompers J, Brüschweiler R. Proteins. 2002;46:177.[PubMed]
136. Amadei A, Linssen A, Berendsen H. Proteins. 1993;17:412.[PubMed]
137. Schäfer H, Mark A, van Gunsteren W. J Chem Phys. 2000;113:7809.[PubMed]
138. Schafer H, Daura X, van Gunsteren W. Proteins. 2001;43:45.[PubMed]
139. Smith P, van Gunsteren W. J Mol Biol. 1994;236:629.[PubMed]
140. Lipari G, Szabo A. J Am Chem Soc. 1982;104:4546.[PubMed]
141. Levy R, Karplus M, Wolynes P. J Am Chem Soc. 1981;103:5998.[PubMed]
142. Palmer A, Case D. J Am Chem Soc. 1992;114:9059.[PubMed]
143. Peter C, Daura X, vanGunsteren W. J Biomol NMR. 2001;20:297.[PubMed]
144. Prompers J, Brüschweiler R. J Am Chem Soc. 2001;123:7305.[PubMed]
145. Prompers J, Brüschweiler R. J Am Chem Soc. 2002;124:4522.[PubMed]