常用分子力学与力场的参考文献

常用分子力学与力场的参考文献

Molecular Mechanics and Force Field References
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AMBER, Assisted Model Building and Energy Refinement
AMBER/OPLS, The AMBER force field with Jorgensen's OPLS parameters
CHARMM, Chemistry at HARvard Macromolecular Mechanics
DISCOVER, force fields of the Insight/Discover package
ECEPP/2, a pairwise potential for proteins and peptides
GROMOS, GROningen MOlecular Simulation package
MM2, the class 1 Allinger molecular mechanics program
MM3, the class 2 Allinger molecular mechanics program
MM4, the class 3 Allinger molecular mechanics program
MMFF94, the Merck Molecular Force Field
Tripos, the force field of the Sybyl molecular modeling program
Comparisons and Evaluations of Force Fields

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AMBER:
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., and Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids and organic molecules, J. Am. Chem. Soc. 117, 5179-5197.
Pearlman, D. A., Case, D. A., Caldwell, J. C., Seibel, G. L., Singh, U. C., Weiner, P., & Kollman, P. A., (1991) AMBER 4.0, University of California, San Francisco.
Weiner, P. K., & Kollman, P. A., (1981) AMBER: Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions, J. Comp. Chem. 2, 287-303.
Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., Jr., Weiner, P.K. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.
Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A., (1986) "An All Atom Force Field for Simulations of Proteins and Nucleic Acids," J. Comp. Chem. 7, 230-252.

AMBER/OPLS:
Damm, W., A. Frontera, J. Tirado-Rives and W. L. Jorgensen (1997) "OPLS All-Atom Force Field for Carbohydrates," J. Comp. Chem. 18, 1955-1970.
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, 11225-11236.
Jorgensen, W. L., & Tirado-Rives, J.,(1988) The OPLS Potential Functions for Proteins. Energy Minimizatio