Accurate and efficient corrections for missing dispersion interactions in molecular simulations

Journal of Physical Chemistry B

Volumn 111, Issue 45, 2007, Pages 13052-13063

  Shirts, Michael R ^a   Mobley, David L ^b   Chodera, John D ^c   Pande, Vijay S ^c  

^a Columbia University ^*  (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISPERSIONS; FREE ENERGY; LIGANDS; MACROMOLECULES; POTENTIAL ENERGY;

ISOTROPIC SYSTEMS; LIGAND BINDING; MOLECULAR DISPERSION; MOLECULAR SIMULATIONS;

MOLECULAR DYNAMICS;

EID: 36649007647     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0735987     Document Type: Article

References (69)

1. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
2. Tuckerman, M.; Berne, B. J.; Martyna, G. J. J. Chem. Phys. 1992, 97, 1990-2001.
3. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317.
4. Steinbach, P. J.; Brooks, B. R. J. Comp. Chem. 1994, 15, 667-683.
5. Sagui, C.; Darden, T. A. Ann. Rev. Biophys. Biomol. Struct. 1999, 28, 155-179.
6. Deserno, M.; Holm, C. J. Chem. Phys. 1998, 109, 7678-7693.
7. Kitchen, D. B.; Hirata, F.; Westbrook, J. D.; Levy, R. M.; Kofke, D.; Yarmush, M. J. Comp. Chem. 1990, 11, 1169.
8. Guenot, J.; Kollman, P. A. J. Comp. Chem. 1993, 14, 295-311.
9. Hünenberger, P. H.; Börjesson, U.; Lins, R. D. Chimia 2001, 55, 861-866.
10. Lisal, M.; Kolafa, J.; Nezbeda, I. J. Chem. Phys. 2002, 117, 8892-8897.
11. Mark, P.; Nilsson, L. J. Comp. Chem. 2002, 23, 1211-1219.
12. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. J. Chem. Phys. 1995, 102, 5451-5459.
13. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: New York, 1987.
14. Shirts, M. R. Ph.D. Dissertation, Stanford University, 2005.
15. Head-Gordon, T.; Hura, G. Chem. Rev. 2002, 102, 2651-2670.
16. Hura, G.; Russo, D.; Glaeser, R. M.; Head-Gordon, T.; Krack, M.; Parrinello, M. Phys. Chem. Chem. Phys. 2003, 5, 1981-1991.
17. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. J. Chem. Phys. 2004, 120, 9665-9678.
18. Kollman, P. A.; Dixon, R.; Cornell, W.; Fox, T.; Chipot, C.; Pohorille, A. The development/application of a 'minimalist' organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. In Computer Simulation of Biomolecular Systems, Vol. 3; Wilkinson, A., Weiner, P., van Gunsteren, W. F., Eds.; Elsevier: Amsterdam, The Netherlands, 1997.
19. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
20. Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. J. Chem. Phys. 2003, 119, 5740-5761.
21. Personal communication.
22. GROMACS manuals 3.1.1, 3.2, or 3.3, at http://www.gromacs.org/gromacs/ documentation/paper-manuals.html.
23. Lagüe, P.; Pastor, R. W. J. Phys. Chem. B 2004, 108, 363-368.
24. van Gunsteren, W. F.; Berendsen, H. J. C. Angew. Chem., Int. Ed. Engl. 1990, 29, 992-1023.
25. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72, 1047-1069.
26. Mobley, D. L.; Chodera, J. D.; Dill, K. A. J. Chem. Phys. 2006, 125, 084902.
27. Straatsma, T. P.; McCammon, J. A. J. Chem. Phys. 1991, 95, 1175-1188.
28. Bennett, C. H. J. Comp. Phys. 1976, 22, 245-268.
29. Shirts, M. R.; Bair, E.; Hooker, G.; Pande, V. S. Phys. Rev. Lett. 2003, 91, 140601.
30. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
31. The derivation of the WHAM estimator used here, eq 21 of ref 30, is too involved to reproduce here, so we refer the reader there for a detailed exposition.
32. Chodera, J. D.; Swope, W. C.; Pitera, J. W.; Seok, C.; Dill, K. A. J. Chem. Theor. Comput. 2007, 3, 26-41.
33. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420-1426.
34. Shirts, M. R.; Pande, V. S. J. Chem. Phys. 2005, 122, 144107.
35. Lu, N. D.; Kofke, D. A. J. Chem. Phys. 2001, 114, 7303-7311.
36. Lu, N. D.; Kofke, D. A. J. Chem. Phys. 2001, 115, 6866-6875.
37. Janke, W. Statistical analysis of simulations: Data correlations and error estimation. In Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms, Vol. 10; Grostendorst, J., Marx, D., Murmatsu, A., Eds.; Rolduc Conference Centre: Kerkrade, The Netherlands, 2002.
38. Shirts, M.; Pande, V. S. Science 2000, 290, 1903-1904.
39. Jayachandran, G.; Shirts, M. R.; Park, S.; Pande, V. S. J. Chem. Phys. 2006, 125, 084901.
40. Shirts, M. R.; Pande, V. S. J. Chem. Phys. 2005, 122, 134508.
41. 40 was orders of magnitude smaller than the uncertainty but became sigificant with the large proteins in this study.
42. Holt, D. A.; Luengo, J. I.; Yamashita, D. S.; Oh, H. J.; Konialian, A. L.; Yen, H. K.; Rozamus, L. W.; Brandt, M.; Bossard, M. J.; Levy, M. A.; Eggleston, D. S.; Liang, J.; Schultz, L. W.; Stout, T. J.; Clardy, J. J. Am. Chem. Soc. 1993, 115, 9925-9938.
43. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637-649.
44. Miyamoto, S.; Kollman, P. A. J. Comp. Chem. 1992, 13, 952-62.
45. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. J. Chem. Phys. 2004, 120, 9665-78.
46. Andersen, H. C. J. Comp. Phys. 1983, 52, 24-34.
47. Andersen, H. C. J. Chem. Phys. 1980, 72, 2384-2393.
48. Sorin, E. J.; Pande, V. S. Biophys. J. 2005, 85, 2472-2493.
49. Fujitani, H.; Tanida, Y.; Ito, M.; Shirts, M. R.; Jayachandran, G.; Snow, C. D.; Pande, E. J. S. V. S. J. Chem. Phys. 2005, 123, 084108.
50. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comp. Chem. 2004, 25, 1157-1174.
51. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. J. Comp. Chem. 2000, 21, 132-46.
52. Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. J. Phys. Chem. A 2003, 107, 9535-9551.
53. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comp. Chem. 2005, 26, 1701-1718.
54. Chambers, C. C.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. A 1996, 100, 16385-16398.
55. Kollman, P. A. Acc. Chem. Res. 1996, 29, 461-469.
56. Liu, D. C.; Nocedal, J. Math. Prog. B 1989, 45, 503-528.
57. We found that the L-BFGS minimizer in GROMACS occasionally terminates extremely early, after only a few steps, so we used additional steepest descents minimization to ensure that minimization was adequate.
58. Hess, B.; Bekker, H.; Berendsen, H. J. C. J. Comp. Chem. 1997, 18, 1463-1472.
59. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3584-3690.
60. Mobley, D. L.; Chodera, J. D.; Dill, K. A. J. Chem. Theor. Comput. 2007, 3, 1231-1235.
61. The listed uncertainties are actually slightly higher for L2 than for L20 using the 0.75-0.9 and 0.9-1.0 cutoffs, but this is principally because of the smaller number of samples collected for L2 at these cutoffs.
62. Morton, A.; Matthews, B. W. Biochemistry 1995, 34, 8576-8588.
63. Morton, A.; Baase, W. A.; Matthews, B. W. Biochemistry 1995, 34, 8564-8575.
64. Wei, B. Q.; Baase, W. A.; Weaver, L. H.; Matthews, B. W.; Shoichet, B. K. J. Mol. Biol. 2002, 322, 339-355.
65. Graves, A. P.; Brenk, R.; Shoichet, B. K. J. Med. Chem. 2005, 48, 3714-3728.
66. Mobley, D. L.; Graves, A. P.; McReynolds, A. C.; Shoichet, B. K.; Dill, K. A. J. Mol. Biol. 2007, 371, 1118-1134.
67. Koo, E. H.; Peter T. Lansbury, J.; Kelly, J. W. Proc. Natl. Acad. Sci., USA. 1999, 96, 9989-9990.
68. If different cutoffs are used to compute the free energies of the complexed ligand and solvated ligand, this cancellation of error will not fully occur, and omitting a proper treatment of the long-range correction will lead to even larger errors in the total binding free energy than exist between columns five and six of Table 3.
69. In GROMACS 3.3, the heterogeneous dispersion correction to the chemical potential was implemented and used for these calculations. As discussed in the text, this can lead to inaccuracies, and likely explains part of the larger cutoff-dependence for toluene in lysozyme than the much larger FK506. The fully buried binding site of toluene also may explain part of the larger discrepancy.