Calculation of relative solvation free energy differences by thermodynamic perturbation method: Dependence of free energy results on simulation length

Journal of Computational Chemistry

Volumn 20, Issue 10, 1999, Pages 1018-1027

  Reddy, M Rami ^a   Erion, Mark D ^a  

^a Metabasis Therapeutics Inc   (United States)

Author keywords

Amber force field; Convergence; Molecular dynamics simulations; Solvation free energies; Thermodynamic cyclic perturbation approach; Thread method

Indexed keywords

EID: 0008747546     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(19990730)20:10<1018::AID-JCC4>3.0.CO;2-B     Document Type: Article

References (32)

1. (a) Zwanzig, R. W. J Chem Phys 1954, 22, 1420-1426;
2. (b) Tembe, B. L.; McCammon, J. A. Comput Chem 1982, 8, 281-283;
3. (c) Beveridge, D. L.; DiCapua, F. M. Annu Rev Biophys Biophys Chem 1989, 18, 431-492;
4. (d) Van Gunsteren, W. F.; Weiner, P. K., Computer Simulation of Biomolecular Systems; ESCOM Science: Leiden, The Netherlands, 1989;
5. (e) Hermans, J., ed. Molecular Dynamics and Protein Structure; Polycrystal: West Springs, IL, 1985;
6. (f) Reddy, M. R.; Bacquet, R. J.; Varney, M. D. J Chem Phys 1991, 88, 2605-2615;
7. (g) Jorgensen, W. L.; Briggs, J. M. J Am Chem Soc 1989, 111, 4190-4197;
8. (h) Nagy, P. I.; Durant, G. J.; Smith, D. A. J Am Chem Soc 1993, 115, 2912-2922;
9. (i) Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A. Science 1987, 235, 574-575;
10. (j) Cieplak, P.; Bash, P.; Singh, U. C.; Kollman, P. A. J Am Chem Soc 1987, 109, 6283-6289;
11. (k) Reddy, M. R.; Viswanadhan, V. N.; Weinstein, J. N. Proc Natl Acad Sci USA 1991, 88, 10287-10291.
12. (a) Mitchell, M. J.; McCammon, J. A. J Comput Chem 1991, 12, 271-275;
13. (b) Pearlman, D. A.; Kollman, P. A. J Chem Phys 1991, 94, 4532-4545;
14. (c) Guarnieri, F.; Still, W. C. J Comput Chem 1994, 15, 1302-1310;
15. (d) Pearlman, D. A. J Comput Chem 1994, 15, 105-123;
16. (e) Chipot, C.; Millot, C.; Maigret, B.; Kollman, P. A. J Phys Chem 1994, 98, 11362;
17. (f) Chipot, C.; Kollman, P. A.; Pearlman, D. A. J Comput Chem 1996, 17, 1112-1131.
18. (a) Erion, M. D.; Reddy, M. R. J Comput Chem 1995, 16, 1513-1521;
19. (b) Erion, M. D.; Reddy, M. R. J Am Chem Soc 1998, 120, 3295-3304.
20. (a) Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagoha, G.; Profeta, S., Jr.; Weiner, P. K. J Am Chem Soc 1984, 106, 765-784;
21. (b) Singh, U. C.; Weiner, P. K.; Caldwell, J. K.; Kollman, P. A. AMBER, Version 3.3, University of California at San Francisco, San Francisco, CA, 1992.
22. Chirlian, L. E.; Francl, M. M. J Comput Chem 1987, 8, 894-905.
23. (a) Frisch, M. J.; Head-Gordon, M.; Schlegel, H. B.; Raghavachari, K.; Binkley, J. S.; Gonzalez, C.; Defrees, D. J.; Fox, D. J.; Whiteside, R. J.; Seeger, R.; Melius, C. F.; Baker, J.; Martin, R.; Kahn, L. R.; Stewart, J. J. P.; Fluder, E. M.; Topiol, S.; Pople, J. A. GAUSSIAN-92; Gaussian, Inc.: Pittsburgh, PA, 1992;
24. (b) Foresman, J. B.; Frisch, A. Exploring Chemistry with Electronic Structure Methods: A Guide to Using GAUSSIAN; Gaussian, Inc.: Pittsburgh, PA, 1993.
25. (a) Berendsen, H. J. C; Grigera, J. R.; Straatsma, T. P. J Phys Chem 1987, 91, 6269-6271;
26. (b) Rami Reddy, M.; Berkowitz, M. Chem Phys Lett 1989, 155, 173-176.
27. (a) Singh, U. C.; Benkovic, S. J. Proc Natl Acad Sci USA 1988, 85, 9519-9523;
28. (b) Rami Reddy, M.; Bacquet, R. J.; Zichi, D.; Matthews, D. A.; Welsh, K. M.; Jones, T. R.; Freer, S. J Am Chem Soc 1992, 114, 10117-10122.
29. Verlet, L. Phys Rev 1967, 159, 98-103.
30. Ryckart, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327-341.
31. (a) Hine, J.; Mookerjee, P. K. J Org Chem 1975, 40, 292-298;
32. (b) Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. J Sol Chem 1981, 10, 563-595.