New out-of-plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations

Journal of Computational Chemistry

Volumn 20, Issue 10, 1999, Pages 1067-1084

  Lee, Sang Ho ^a   Palmo, Kim ^a   Krimm, Samuel ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Internal coordinates; Molecular dynamics; Molecular mechanics; Potential energy functions

Indexed keywords

EID: 0001048830     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(19990730)20:10<1067::AID-JCC9>3.0.CO;2-V     Document Type: Article

References (30)

1. Lee, S.-H.; Krimm, S. Biopolymers 1998, 46, 283.
2. Palmo, K.; Mirkin, N. G.; Krimm, S. J Phys Chem 1998, A102, 6448.
3. MacKerell, A. D., Jr.; Bashford, D.; Bellott, 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 1998, B102, 3586.
4. Maple, J. R.; Hwang, M.-J.; Jalkanen, K. J.; Stockfisch, T. P.; Hagler, A. T. J Comput Chem 1998, 19, 430.
5. Halgren, T. A. J Comput Chem 1996, 17, 553.
6. Nevins, N.; Chen, K.; Allinger, N. L. J Comput Chem 1996, 17, 669.
7. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
8. Wilson, E. B.; Decius, J. C.; Cross, P. C. In Molecular Vibrations; McGraw-Hill: New York, 1955.
9. Schlick, T. J Comput Chem 1989, 10, 951.
10. Noid, D. W.; Sumpter, B. G.; Wunderlich, B.; Pfeffer, G. A. J Comput Chem 1990, 11, 236.
11. Swope, W. C.; Ferguson, D. M. J Comput Chem 1992, 13, 585.
12. Blondel, A.; Karplus, M. J Comput Chem 1996, 17, 1132.
13. Tuzun, R. E.; Noid, D. W.; Sumpter, B. G. Macromol Theory Simul 1995, 4, 909.
14. Miller, K. J.; Hinde, R. J.; Anderson, J. J Comput Chem 1989, 10, 63.
15. Miller, K. J. J Comput Chem 1990, 11, 336.
16. Lee, S.-H. Ph.D. thesis, University of Michigan (1997).
17. Tuzun, R. E.; Noid, D. W.; Sumpter, B. G. J Comput Chem 1997, 18, 1804.
18. Plíva, J. Coll Czech Chem Commun 1958, 23, 777.
19. Dennison, D. M.; Uhlenbeck, G. E. Phys Rev 1932, 41, 313.
20. Califano, S. In Vibrational States; Wiley: New York, 1976.
21. Mills, I. M. Chem Phys Lett 1969, 3, 267.
22. Palmo, K.; Pietilä, L.-O.; Krimm, S. J Comput Chem 1992, 13, 1142.
23. Rush, D. J.; Wiberg, K. B. J Phys Chem 1997, A101, 3143.
24. Császár, A. G.; Allen, W. D.; Schaefer, H. F., III J Chem Phys 1998, 108, 9751.
25. Dennison, D. M.; Hardy, J. D. Phys Rev 1932, 39, 938.
26. Papousek, D.; Stone, J. M. R.; Spirko, V. J Mol Spectrosc 1973, 48, 17.
27. Spirko, V. J Mol Spectrosc 1983, 101, 30.
28. Koput, J. Chem Phys 1990, 148, 299.
29. Durig, J. R.; Flanagan, M. J.; Kalasinsky, V. F. J Chem Phys 1977, 66, 2775.
30. Sun, H.; Rigby, D. Spectrochim Acta 1997, A53, 1301.