The role of bonded energy terms in free energy simulations - Insights from analytical results

Molecular Simulation

Volumn 28, Issue 1-2, 2002, Pages 13-37

  Boresch, Stefan ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

Dummy atoms; Jacobian factor contribution; Potential of mean force like contribution; Thermodynamic integration; Vibrational contribution

Indexed keywords

ATOMS; CHEMICAL BONDS; COMPUTER SIMULATION; ORGANIC COMPOUNDS; THERMODYNAMIC PROPERTIES; TOPOLOGY;

DUMMY ATOMS; JACOBIAN FACTOR CONTRIBUTION; POTENTIAL-OF-MEAN-FORCE-LIKE CONTRIBUTION; THERMODYNAMIC INTEGRATION; VIBRATIONAL CONTRIBUTION;

FREE ENERGY;

EID: 0141536248     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020211969     Document Type: Article

References (53)

1. Kollman, P. (1993). "Free energy calculations: Applications to chemical and biochemical phenomena", Chem. Rev., 93, 2395.
2. Kollman, P. A. (1996). "Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules", Accounts Chem. Res., 29, 461.
3. Straatsma, T. P., "Free energy by molecular simulation", In: Reviews in Computational Chemistry, Lipkowitz, K. B. and Boyd, D. B. Eds., VCH, New York, 1996, 9, 81-127.
4. Kirkwood, J. G. (1935). "Statistical mechanics of fluid mixtures", J. Chem. Phys., 3, 300.
5. Zwanzig, R. W. (1954). "High-temperature equation of state by a perturbation method. I. Nonpolar gases", J. Chem. Phys., 22, 1420.
6. Simonson, T. (1993). "Free energy of particle insertion: An exact analysis of the origin singularity for simple liquids", Mol. Phys., 80, 441.
7. Zacharias, M., Straatsma, T. P. and McCammon, J. A. (1994). "Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration", J. Chem. Phys., 100, 9025.
8. Beutler, T. C., Mark, A. E., van Schaik, R. C., Gerber, P. R. and van Gunsteren, W. F. (1994). "Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations", Chem. Phys. Lett., 222, 529.
9. Pomès, R., Eisenmesser, E., Post, C. B. and Roux, B. (1999). "Calculating excess chemical potentials using dynamic simulations in the fourth dimension", J. Chem. Phys., 111, 3387.
10. Brunsteiner, M. and Boresch, S. (2000). "Influence of the treatment of electrostatic interactions on the results of free energy calculations of dipolar systems", J. Chem. Phys., 112, 6953.
11. Rozanska, X. and Chipot, C. (2000). "Modeling ion-ion interactions in proteins: A molecular dynamics free energy calculation of the guanidinum-acetate association", J. Chem. Phys., 112, 9691.
12. Simonson, T. (2000). "Electrostatic free energy calculations for macromolecules: A hybrid molecular dynamics/continuum electrostatics approach", J. Phys. Chem. B, 104, 6509.
13. den Otter, W. K. and Briels, W. J. (1998). "The calculation of free-energy differences by constrained molecular-dynamics simulations", J. Chem. Phys., 109, 4139.
14. Boresch, S. and Karplus, M. ( 1999). "The role of bonded terms in free energy simulations: 1. theoretical analysis", J. Phys. Chem. A, 103, 103.
15. Boresch, S. and Karplus, M. (1999). "The role of bonded terms in free energy simulations. 2. calculation of their influence on free energy differences of solvation", J. Phys. Chem. A, 103, 119.
16. Shobana, S., Roux, B. and Andersen, O. S. (2000). "Free energy simulations: Thermodynamic reversibility and variability", J. Phys. Chem. B, 104, 5179.
17. Pearlman, D. A. and Kollman, P. A. (1991). "The overlooked bond-stretching contribution in free energy perturbation calculations", J. Chem. Phys., 94, 4532.
18. Straatsma, T. P., Zacharias, M. and McCammon, J. A. (1992). "Holonomic constraint contributions to free energy differences from thermodynamic integration molecular dynamics simulations", Chem. Phys. Lett., 196, 297.
19. Wang, L. and Hermans, J. (1994). "Change of bond length in free-energy simulations: Algorithmic improvements, but when is it necessary", J. Chem. Phys., 100, 9129.
20. Severance, D. L., Essex, J. W. and Jorgensen, W. L. (1995). "Generalized alteration of structure and parameters: A new method for free-energy perturbations in systems containing flexible degrees of freedom", J. Comput. Chem., 16, 311.
21. Axelsen, P. H. and Li, D. (1998). "Improved convergence in dual-topology free energy calculations through use of harmonic restraints", J. Comput. Chem., 19, 1278.
22. Reddy, M. R., Erion, M. D., Agarwal, A., Viswanadhan, V. N., McDonald, D. Q. and Still, W. C. (1998). "Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields", J. Comput. Chem., 19, 769.
23. Prévost, M., Wodak, S. J., Tidor, B. and Karplus, M. (1991). "Contribution of the hydrophobic effect to protein stability: Analysis based on simulations of the He 96→ Ala mutation in barnase", Proc. Natl. Acad. Sci. USA, 88, 10880.
24. 2 substrate binding. A study of the influence of simulation length, internal degrees of freedom and structure in free energy perturbations", Mol. Simulation, 10, 255.
25. Harris, D. and Loew, G. (1996). "Comparative study of free energies of solvation of phenylimidazole inhibitors of cytochrome P450cam by free energy simulation, AMSOL and Poisson Boltzmann methods", J. Comput. Chem., 17, 273.
26. Rao, B. G., Kim, E. E. and Murcko, M. A. (1996). "Calculation of solvation and binding free energy differences between VX-488 and its analogs by free energy perturbation and AMSOL methods", J. Comput.-Aided Mol. Design, 10, 23.
27. Sun, Y.-C., Vcenstra, D. L. and Kollman, P. A. (1996). "Free energy calculations of the mutation of Ile96→ Ala in barnase: contributions to the difference in stability", Prot. Eng., 9, 273.
28. Pearlman, D. A. (1994). "A comparison of alternative approaches to free energy calculations", J. Phys. Chem., 98, 1487.
29. Paci, E., Ciccotti, G., Ferrario, M. and Kapral, R. (1991). "Activation energies by molecular dynamics with constraints", Chem. Phys. Lett., 176, 581.
30. McQuarrie, D. A., Statistical Mechanics, Harper and Row, New York, 1976.
31. Cornell, W. D., Cieplak, P., Bayly, C. I., Could, I. R., Merz, K. M. Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. and Kollman, P. A. (1995). "A second generation force field for the simulation of proteins and nucleic acids", J. Am. Chem. Soc., 117, 5179.
32. van Gunsteren, W. F., Billeter, S. R., Eising, A. A., Hünenberger, P. H., Krüger, P., Mark, A. E., Scott, W. R. P. and Tironi, I. G., Biomolecular Simulation: The GROMOS96 Manual and User Guide, vdf Hochschulverlag, Zürich, 1996.
33. Jorgensen, W. L., Maxwell, D. S. and Tirado-Rives, J. (1996). "Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids", J. Am. Chem. Soc., 118, 11225.
34. 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, III, W. E., Roux, B., Schlenkrich, M., Smith, J., Stole, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D. and Karplus, M. (1998). "All-atom empirical potential for molecular modeling and dynamics studies of protein", J. Phys. Chem. B, 102, 3586.
35. DeVoe, H., "Theory of the conformations of biological macromoleculcs in solution", In: Structure and Stability of Biological Macromoleculs, Timascheff, S, N. and Fasman, G. D. Eds., Dekker, New York, 1969, 1, 1-63.
36. Herschbach, D. R., Johnston, H. S. and Rapp, D. (1959). "Molecular partition functions in terms of local properties", J. Chem, Phys., 31, 1652.
37. Gō, N. and Scheraga, H. A. (1976). "On the use of classical statistical mechanics in the treatment of polymer chain conformation", Macromolecules, 9, 535.
38. Wilson, E. B. Jr., Decius, J. C. and Cross, P. C, Molecular Vibrations. The Theory of Infrared and Raman Vibrational Spectra, McGraw-Hill, New York, 1955.
39. Boresch, S. and Karplus, M. (1996). "The Jacobian factor in free energy simulations", J. Chem. Phys., 105, 5145.
40. Tembe, B. L. and McCammon, J. A. (1984). "Ligand-receptor interactions", Comput. Chem., 8, 281.
41. Pearlman, D. A. (1993). "Determining the contributions of constraints in free energy calculations: Development, characterization, and recommendations", J. Chem. Phys., 98, 8946.
42. Pearlman, D. A., Case, D. A., Caldwell, J. W., ROSS, W. S., Cheatham III, T. E., Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K. and Kollman, P., AMBER 4.1, University of California, San Francisco, 1995.
43. McCammon, J. A. (1998). "Theory of biomolecular recognition", Curr. Op. Struct, Biol., 8, 245.
44. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. and Karplus, M. (1983). "CHARMM: A program for macromolecular energy, minimization and dynamics calculations", J. Comput. Chem., 4, 187.
45. Simonson, T. and Brünger, A. T. (1992). "Thermodynamics of protein-peptide interactions in the Ribonuclease-S system studied by molecular dynamics and free energy calculations", Biochemistry, 31, 8661.
46. Neria, E., Fischer, S. and Karplus, M. (1996). "Simulation of activation free energies in molecular systems", J. Chem. Phys., 105, 1902.
47. Ryckaert, J. P., Ciccotti, G. and Berendsen, H. J. C. (1997). "Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes", J. Comput. Phys., 23, 327.
48. Hermans, J. and Wang, L. (1997). "Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 Lysozyme", J. Am. Chem. Soc., 119, 2707.
49. Hoover, W. G. (1985). "Canonical dynamics: Equlibrium phase-space distributions", Phys. Rev., A31, 1695.
50. Zachmann, H. G., Mathematik für Chemiker, Verlag Chemie, Wcinheim, 1984.
51. Ben-Nairn, A. and Marcus, Y. J. (1984). "Solvation thermodynamics of nonionic solutes", J. Chem. Phys., 81, 2016.
52. Mohamadi, F., Richards, N. G. J., Guida, W. C., Liskamp, R., Lipton, M., Caufield, C., Chang, G., Hendrickson, T. and Still, W. C. (1990). "MacroModel - an integrated software system for modeling organic and bioorganic molecules using molecular mechanics", J. Comput. Chem., 11, 440.
53. Jorgensen, W. L., "BOSS - Biochemical and organic simulation system", In: The Encyclopedia of Computational Chemistry, Schleyer, P. v. R. Ed., Wiley, Athens, USA, 1998, 3, 3281-3285.