A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6

Journal of Computational Chemistry

Volumn 25, Issue 13, 2004, Pages 1656-1676

  Oostenbrink, Chris ^a   Villa, Alessandra ^b   Mark, Alan E ^b   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

Force field parameterization; Free energy calculation; GROMOS force field; Hydration; Solvation

Indexed keywords

BIOLOGICAL MEMBRANES; COMPUTER SIMULATION; ENTHALPY; FREE ENERGY; HAMILTONIANS; HYDRATION; KINETIC ENERGY; THERMODYNAMIC PROPERTIES;

FORCE-FIELD PARAMETRIZATION; FREE-ENERGY CALCULATION; GROMOS FORCE FIELD; SOLVATION;

BIOMATERIALS;

AMINO ACID; CYCLOHEXANE DERIVATIVE; SOLVENT; WATER;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; ENERGY TRANSFER; PROTEIN FOLDING; THERMODYNAMICS;

ALGORITHMS; AMINO ACIDS; COMPUTER SIMULATION; CYCLOHEXANES; ENERGY TRANSFER; MODELS, CHEMICAL; PROTEIN FOLDING; SOLVENTS; THERMODYNAMICS; WATER;

EID: 4444282928     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20090     Document Type: Article

References (92)

1. Hünenberger, P. H.; van Gunsteren, W. F. In Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications; van Gunsteren, W. F.; Weiner, P. K.; Wilkinson, A. J., Eds.; Kluwer Academic Publishers: Dordrecht, 1997, p. 3.
2. Hünenberger, P. H.; van Gunsteren, W. F. In Potential Energy Surfaces; Sax, A. P., Ed.; Springer: Berlin, 1999, p. 177.
3. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
4. MacKerell, A. D., Jr.; Bashford, D.; Bellot, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
5. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J Am Chem Soc 1996, 118, 11225.
6. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Vdf Hochschulverlag AG an der ETH Zürich: Zürich, 1996.
7. Hagler, A. T.; Ewig, C. S. Comput Phys Commun 1994, 84, 131.
8. Weerasinghe, S.; Smith, P. E. J Chem Phys 2003, 118, 10663.
9. Schuler, L. D.; Daura, X.; van Gunsteren, W. F. J Comput Chem 2001, 22, 1205.
10. Weiner, P. K.; Kollman, P. A. J Comput Chem 1981, 2, 287.
11. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., III; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. A. Comput Phys Comm 1995, 91, 1.
12. MacKerell, A. D., Jr.; Wiórkiewicz-Kuczera, J.; Karplus, M. J Am Chem Soc 1995, 117, 11946.
13. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187.
14. Momany, F. A.; Rone, R. J Comput Chem 1992, 13, 888.
15. Nemethy, G.; Gibson, K. D.; Palmer, K. A.; Yoon, C. N.; Paterlini, G.; Zagari, A.; Rumsey, S.; Scheraga, H. A. J Phys Chem 1992, 96, 6472.
16. Levitt, M. J Mol Biol 1983, 168, 595.
17. Levitt, M.; Hirshberg, M.; Sharon, R.; Daggett, V. Comput Phys Comm 1995, 91, 215.
18. van Gunsteren, W. F.; Berendsen, H. J. C. Groningen Molecular Simulation (GROMOS) Library Manual; Biomos: Groningen, 1987.
19. Jorgensen, W. L.; Tirado-Rives, J. J Am Chem Soc 1988, 110, 1657.
20. Hermans, J.; Berendsen, H. J. C.; van Gunsteren, W. F.; Postma, J. P. M. Biopolymers 1984, 23, 1513.
21. Smith, L. J.; Mark, A. E.; Dobson, C. M.; van Gunsteren, W. F. Biochemistry 1995, 34, 10918.
22. Daura, X.; Mark, A. E.; van Gunsteren, W. F. J Comput Chem 1998, 19, 535.
23. van Gunsteren, W. F.; Daura, X.; Mark, A. E. In Encyclopedia of Computational Chemistry; von Ragué Schleyer, P., Ed.; John Wiley & Sons: New York, 1998, p. 1211.
24. Schuler, L. D.; van Gunsteren, W. F. Mol Sim 2000, 25, 301.
25. Chandrasekhar, I.; van Gunsteren, W. F. Curr Sci 2001, 81, 1325.
26. Chandrasekhar, I.; van Gunsteren, W. F. Eur Biophys J 2002, 31, 89.
27. Chandrasekhar, I.; Kastenholz, M. A.; Lins, R. D.; Oostenbrink, C.; Schuler, L. D.; Tieleman, D. P.; van Gunsteren, W. F. Eur Biophys J 2003, 32, 67.
28. Daura, X.; van Gunsteren, W. F.; Rigo, D.; Jaun, B.; Seebach, D. Chem Eur J 1997, 3, 1410.
29. Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Angew Chem In Ed 1999, 38, 236.
30. van Gunsteren, W. F.; Bürgi, R.; Peter, C.; Daura, X. Angew Chem In Ed 2001, 40, 351.
31. Daura, X.; Glättli, A.; Gee, P.; Peter, C.; van Gunsteren, W. F. Adv Protein Chem 2002, 62, 341.
32. Bakowies, D.; van Gunsteren, W. F. J Mol Biol 2002, 315, 713.
33. Stocker, U.; van Gunsteren, W. F. Proteins 2000, 40, 145.
34. Stocker, U.; Spiegel, K.; van Gunsteren, W. F. J Biomol NMR 2000, 18, 1.
35. Smith, L. J.; Dobson, C. M.; van Gunsteren, W. F. J Mol Biol 1996, 286, 1567.
36. Smith, L. J.; Dobson, C. M.; van Gunsteren, W. F. Proteins 1999, 36, 77.
37. Antes, I.; Thiel, W.; van Gunsteren, W. F. Eur Biophys J 2002, 31, 504.
38. Oostenbrink, B. C.; Pitera, J. W.; Van Lipzig, M. M. H.; Meerman, J. H. N.; van Gunsteren, W. F. J Med Chem 2000, 43, 4594.
39. Bonvin, A. M.; Sunnerhagen, M.; Otting, G.; van Gunsteren, W. F. J Mol Biol 1998, 282, 859.
40. Czechtizky, W.; Daura, X.; Vasella, A.; van Gunsteren, W. F. Helv Chim Acta 2001, 84, 2132.
41. van Gunsteren, W. F.; Mark, A. E. J Chem Phys 1998, 108, 6109.
42. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B. E., Ed.; Reidel: Dordrecht, The Netherlands, 1981, p. 331.
43. Glättli, A.; Daura, X.; van Gunsteren, W. F. J Chem Phys 2002, 116, 9811.
44. Tironi, I. G.; van Gunsteren, W. F. Mol Phys 1994, 83, 381.
45. Walser, R.; Mark, A. E.; van Gunsteren, W. F.; Lauterbach, M.; Wipff, G. J Chem Phys 2000, 112, 10450.
46. Liu, H. Y.; Müller-Plathe, F.; van Gunsteren, W. F. J Am Chem Soc 1995, 117, 4363.
47. Geerke, D. P.; Oostenbrink, C.; van der Vegt, N. F. A.; van Gunsteren, W. F. J Phys Chem B 2004, 108, 1436.
48. Tironi, I. G.; Fontana, P.; van Gunsteren, W. F. Mol Sim 1996, 18, 1.
49. Lins, R. D.; Hünenberger, P. H. Unpublished results.
50. Villa, A.; Mark, A. E. J Comput Chem 2002, 23, 548.
51. Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. J Chem Phys 2003, 119, 5740.
52. MacCallum, J. L.; Tieleman, D. P. J Comput Chem 2003, 24, 1930.
53. Soares, T.; van Gunsteren, W. F. Unpublished results.
54. Fioroni, M.; Burger, K.; Mark, A. E.; Roccatano, D. J Phys Chem B 2000, 104, 12347.
55. Smith, L. J.; Berendsen, H. J. C.; van Gunsteren, W. F. J Phys Chem A 2004, 108, 1065.
56. Scott, W. R. P.; Hünenberger, P. H.; Tironi, I. G.; Mark, A. E.; Billeter, S. R.; Fennen, J.; Torda, A. E.; Huber, P.; Krüger, P.; van Gunsteren, W. F. J Phys Chem A 1999, 103, 3596.
57. CRC Handbook of Chemistry and Physics: A Ready-Reference Book of Chemical and Physical Data, 52nd ed.; CRC Press, Inc.: Boca Raton, FL, 1952.
58. van Gunsteren, W. F.; Karplus, M. Biochemistry 1982, 21, 2259.
59. Gurskaya, G. V. The Molecular Structure of Amino Acids. Determination by X-ray Diffraction Analysis; Consultants Bureau: New York, 1968.
60. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. J Chem Phys 1995, 102, 5451.
61. Radzicka, A.; Wolfenden, R. Biochemistry 1988, 27, 1664.
62. Wolfenden, R. Biochemistry 1981, 20, 849.
63. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327.
64. Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
65. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput Phys Commun 1995, 91, 43.
66. Lindahl, E.; Hess, B.; van der Spoel, D. J Mol Model 2001, 7, 306.
67. van der Spoel, D.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Hess, B.; Feenstra, K. A.; Lindahl, E.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual Version 3.0: Nijenborgh 4, 9747 AG, Groningen, The Netherlands. Internet: http://www.gromacs.org, 2001.
68. Heinz, T. N.; van Gunsteren, W. F.; Hünenberger, P. H. J Chem Phys 2001, 115, 1125.
69. Beveridge, D. L.; DiCapua, F. M. Annu Rev Biophys Biophys Chem 1989, 18, 431.
70. Beutler, T. C.; Mark, A. E.; Van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Chem Phys Lett 1994, 222, 529.
71. Njo, S. L.; van Gunsteren, W. F.; Müller-Plathe, F. J Chem Phys 1995, 102, 6199.
72. Norrby, P. O.; Liljefors, T. J Comput Chem 1998, 19, 1146.
73. Faller, R.; Schmitz, H.; Biermann, O.; Müller-Plathe, F. J Comput Chem 1999, 20, 1009.
74. Riddick, J. A.; Bunger, W. B.; Sakano, T. K. Organic Solvents, Physical Properties and Methods of Purification; John Wiley & Sons: New York, 1986.
75. Majer, V.; Svoboda, V. Enthalpies of Vaporization of Organic Compounds: A Critical Review and Data Compilation; Blackwell Scientific Publications: Oxford, 1985.
76. Nilsson, S.-O.; Wadsö, I. J Chem Thermodyn 1986, 18, 673.
77. CRC Handbook of Chemistry and Physics: A Ready-Reference Book of Chemical and Physical Data; CRC Press, Inc.: Boca Raton, FL, 2000.
78. Haines, W. E.; Helm, R. V.; Bailey, C. W.; Ball, J. S. J Phys Chem 1954, 58, 270.
79. Haines, W. E.; Helm, R. V.; Cook, G. L.; Ball, J. S. J Phys Chem 1956, 60, 549.
80. Scott, D. W.; Finke, H. L.; Hubbard, W. N.; McCullough, J. P.; Oliver, G. D.; Gross, M. E.; Katz, C.; Williamson, K. D.; Waddington, G.; Huffmann, H. M. J Am Chem Soc 1951, 74, 4656.
81. Wagman, P. D.; Evans, W. H.; Parker, V. B.; Schumm, R. H.; Halow, I.; Bailey, S. M.; Churney, K. L.; Nuttall, R. L. J Phys Chem Ref Data 1982, 11, 1.
82. Guillot, B. J Mol Liq 2002, 101, 219.
83. Price, D. J.; Brooks, C. L., III. J Comput Chem 2002, 23, 1045.
84. Bash, P. A.; Singh, U. C.; Langridge, R.; Kollman, P. A. Science 1987, 236, 564.
85. Jorgensen, W. L.; Briggs, J. M.; Contreras, M. L. J Phys Chem 1990, 94, 1683.
86. Schäfer, H.; van Gunsteren, W. F.; Mark, A. E. J Comput Chem 1999, 20, 1604.
87. Wescott, J. T.; Fisher, L. R.; Hanna, S. J Chem Phys 2002, 116, 2361.
88. Mu, Y.; Stock, G. J Phys Chem B 2002, 106, 5294.
89. Hu, H.; Elstner, M.; Hermans, J. Proteins 2003, 50, 451.
90. Mu, Y.; Kosov, D. S.; Stock, G. J Phys Chem B 2003, 107, 5064.
91. Yu, H. B.; Hansson, T.; van Gunsteren, W. F. J Chem Phys 2003, 118, 221.
92. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J Phys Chem 1987, 91, 6269.