Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations

Journal of Computational Chemistry

Volumn 17, Issue 8, 1996, Pages 1068-1084

  Ott, Karl Heinz ^a,b   Meyer, Bernd ^a,c  

^a UNIVERSITY OF GEORGIA   (United States)

^b PFIZER INC   (United States)

^c UNIVERSITY OF HAMBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000438266     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199606)17:8<1068::AID-JCC14>3.0.CO;2-A     Document Type: Article

References (58)

1. W. F. van Gunsteren and H. J. C. Berendsen, Angew. Chem. Int. Ed. Engl., 29, 992 (1990).
2. S. W. Homans and M. Forster, Glycobiology, 2, 143 (1992).
3. W. F. van Gunsteren, Curr. Opin. Struc. Biol., 3, 277 (1993).
4. J. P. Carver, D. Mandel, S. W. Michnick, A. Imberty, and J. W. Brady, ACS Symp. Ser., 430, 266 (1990).
5. A. T. Brünger and M. Karplus, Acc. Chem., 24, 54 (1991).
6. R. Bruschweiler, B. Roux, M. Blackledge, C. Griesinger, M. Karplus, and R. R. Ernst, J. Am. Chem. Soc., 114, 2289 (1992).
7. W. F. van Gunsteren and A. E. Mark, Eur. J. Biochem., 204, 947 (1992).
8. B. Meyer, Topics Curr. Chem., 154, 141 (1990).
9. I. Tvaroska, S. Pérez, O. Noble, and F.-R. Taravel, Biopolymers, 26, 1499 (1987).
10. J. E. H. Koehler, W. Saenger, and W. F. van Gunsteren, Eur. Biophys. J., 16, 153 (1988).
11. J. E. H. Koehler, W. Saenger, and W. F. van Gunsteren, J. Biomol. Struct. Dynamics, 6, 181 (1988).
12. J. E. H. Koehler, W. Saenger, and W. F. van Gunsteren, J. Mol. Biol, 203, 241 (1988).
13. L. M. J. Kroon-Batenburg and J. Kroon, Biopolymers, 29, 1243 (1990).
14. B. P. van Eijck, L. M. J. Kroon-Batenburg, and J. Kroon, J. Mol. Struct., 237, 315 (1990).
15. H. Beierbeck and R. U. Lemieux, Can. J., 68, 820 (1990).
16. Z. Y. Van and C. A. Bush, Biopolymers, 29, 799 (1990).
17. S. Ha, J. Gao, B. Tidor, J. W. Brady, and M. Karplus, J. Am. Chem. Soc., 113, 1553 (1991).
18. B. J. Hardy and A. Sarko, J. Comput. Chem., 14, 848 (1993).
19. J. W. Brady and R. K. Schmidt, J. Phys. Chem., 97, 958 (1993).
20. S. N. Ha, A. Giammona, M. Field, and J. W. Brady, Carbohydr. Res., 180, 207 (1988).
21. S. W. Homans, Biochemistry, 29, 9110 (1990).
22. N. R. Krishna, B.-Y. Choe, M. Prabhakaran, G. C. Ekborg, L. Rodén, and S. C. Harvey, J. Biol. Chem., 265, 18256 (1990).
23. Z.-Y. Yan, B. N. N. Rao, and C. A. Bush, J. Am. Chem. Soc., 109, 7663 (1987).
24. J. E. H. Koehler, W. Saenger, and W. F. van Gunsteren, Eur. Biophys. J., 15, 97 (1987).
25. J. E. H. Koehler, W. Saenger, and W. F. van Gunsteren, Eur. Biophys. J., 25, 211 (1987).
26. C. J. Edge, U. C. Singh, R. Bazzo, G. L. Taylor, R. A. Dwek, and T. W. Rademacher, Biochemistry, 29, 1971 (1990).
27. J. W. Brady, J. Am. Chem. Soc., 111, 5155 (1989).
28. J. W. Brady, Curr. Opin. Struct. Biol., 1, 711 (1991).
29. S. W. Homans, Biochemistry, 29, 9110 (1990).
30. M. Prabhakaran, Biochem. Biophys. Res. Commun., 178, 192 (1991).
31. G. A. Jeffrey, J. Mol. Struct., 237, 75 (1990).
32. W. F. van Gunsteren and H. J. C. Berendsen, Groningen Molecular Simulation (GROMOS) Library Manual, BIOMOS, Nijenbourgh 16, Groningen, The Netherlands, 1987.
33. A. E. Mark, H. J. C. Berendsen, and W. F. van Gunsteren, Biochemistry, 30, 10866 (1991).
34. R. M. Sok, H. J. C. Berendsen, and W. F. van Gunsteren, J. Chem. Phys., 96, 4699 (1992).
35. W. F. van Gunsteren, H. J. C. Berendsen, R. G. Geurtsen, and H. J. R. Zwinderman, Ann. NY Acad. Sci. USA, 482, 287 (1986).
36. H. Thogersen, R. U. Lemieux, K. Bock, and B. Meyer, Can. J. Chem., 60, 44 (1982).
37. K.-H. Ott and B. Meyer, MD Simulations of Maltose in Water, Carbohydr. Res., to appear.
38. Precision Visuals, Inc. Boulder, CO, 1989.
39. Tripos Associates, Inc., St. Louis, MO, 1992.
40. Digital Equipment Co., Users Reference, Maynard, MA, 1991.
41. G. A. Jeffrey, J. A. Pople, and L. Radom, Carbohydr. Res., 38, 81 (1974).
42. K. B. Wiberg and M. A. Murcko, J. Am. Chem. Soc., 111, 4821 (1989).
43. B. Meyer, Unpublished data, 1990.
44. Linde D. R., Ed., CRC Handbook of Chemistry and Physics, 73rd ed., CRC Press, Boca Raton, FL, 1992-1993, p. 9-7, 9-8.
45. W. F. van Gunsteren and H. J. C. Berendsen, Mol. Phys., 34, 1311 (1977).
46. Lotus 123, Lotus Development Co., Cambridge, MA, release 3.1.
47. SigmaPlot for DOS, Jandel Scientific, San Rafael, CA, 1992.
48. H. J. C. Berendsen, P. J. M. Postma, W. F. van Gunsteren, and J. Hermans, In Intermolecular Forces, B. Pullman, Ed., Reidel, Dordrecht, The Netherlands, 1981, p. 331.
49. H. J. C. Berendsen, P. J. M. Postma, W. F. van Gunsteren, A. di Nola, and J. R. Haak, J. Chem. Phys., 81, 3684 (1984).
50. N. S. Zefirov, V. V. Samoshin, O. A. Subbotin, V. I. Baranenkov, and S. Wolfe, Tetrahedron, 34, 2953 (1978).
51. J.-P. Praly and R. U. Lemieux, Can. J. Chem., 65, 213 (1987).
52. M. A. Murco and R. A. DiPaola, J. Am. Chem. Soc., 114, 10010 (1992).
53. D. A. Smith, R. L. Jaffe, and D. Y. Yon, J. Phys. Chem., 97, 12752 (1993).
54. D. A. Rees and D. Thom, J. Chem. Soc. Perkin Trans. II, 191 (1977).
55. A. Parfondry and N. Cyr. Carbohydr. Res., 59, 299 (1977).
56. G. M. Lipkind, V. E. Verovsky, and N. K. Kochetkov, Carbohydr. Res., 133, 1 (1984).
57. S. Perez, F. Taravel, and C. Vergelati, Nouv. J. Chim., 561 (1985).
58. A. S. Shashkov, G. M. Lipkind, and N. K. Kochetkov, Carbohydr. Res., 147, 175 (1986).