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[转载]常用分子力学与力场的参考文献

Molecular Mechanics and Force Field References


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


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 Minimization for Crystals of Cyclic Peptides and Crambin, J. Am. Chem. Soc. 110, 1657-1666.

Kaminski, G., Duffy, E. M. Matsui, T., and Jorgensen, W. L. (1994) J. Phys. Chem. 98, 13077-13082.

CHARMM: Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. (1983) CHARMM: A program for macromolecular energy, minmimization, and dynamics calculations. J. Comp. Chem. 4, 187-217. Feller et al.,(1997) Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration: Parameterization and Comparison with Diffraction Studies. Biophys. J. 73, 2269-2279

MacKerell, A D Bashford, D; Bellott, M; Dunbrack, R L; Eva seck, J D; Field, M J; Fischer, S; Gao, J; Guo, H; Ha, S; JosephMcCarthy, D; Kuc nir, L; Kuczera, K; Lau, F T K; Mattos, C; Michnick, S; Ngo, T; Nguyen, D T; Pro hom, B; Reiher, W E; Roux, B; Schlenkrich, M; Smith, J C; Stote, R; Straub, J; W tanabe, M; Wiorkiewicz Kuczera, J; Yin, D; Karplus, M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem., B 102, 3586-3617

Mackerell A D Wiorkiewiczkuczera J; Karplus, M (1995) An all-atom empirical energy function for the simulation of nucleic acids. J. Amer. Chem. Soc.117, 11946-11975

Momany, F. A., & Rone, R., (1992) Validation of the General Purpose QUANTA 3.2/CHARMm Force Field, J. Comp. Chem. 13, 888-900.

Pavelites, J. J., J. Gao, P.A. Bash and A. D. Mackerell, Jr. (1997) “A Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate Groups of Nucleotides,” J. Comp. Chem. 18, 221-239.

Schlenkrich et al. (1996), Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and Applications in “Biological Membranes: A Molecular Perspective from Computation and Experiment,” K.M. Merz and B. Roux, Eds. Birkhauser, Boston, pp 31-81, 1996

Discover: cvff- Dauber-Osguthorpe, P.; Roberts, V. A.; Osguthorpe, D. J.; Wolff, J.; Genest, M.; Hagler, A. T. (1988) “Structure and energetics of ligand binding to proteins: E. coli dihydrofolate reductase- trimethoprim, a drug-receptor system”, Proteins: Structure, Function and Genetics, 4, 31-47.

cff- Hagler, A. T.; Ewig, C. S. “On the use of quantum energy su**ces in the derivation of molecular force fields”, Comp. Phys. Comm., 84, 131-155 (1994).

Hwang, M.-J.; Stockfisch, T. P.; Hagler, A. T. “Derivation of Class II force fields. 2. Derivation and characterization of a Class II force field, CFF93, for the alkyl functional group and alkane molecules”, J. Amer. Chem. Soc., 116, 2515-2525 (1994).

Maple, J. R.; Hwang, M.-J.; Stockfisch, T. P.; Dinur, U.; Waldman, M.; Ewig, C. S; Hagler, A. T. " Derivation of Class II force fields. 1. Methodology and quantum force field for the alkyl functional group and alkane molecules", J. Comput. Chem., 15, 162-182 (1994a).

Maple, J. R.; Hwang, M.-J.; Stockfisch, T. P.; Hagler, A. T. “Derivation of Class II force fields. 3. Characterization of a quantum force field for the alkanes”, Israel J. Chem., 34, 195 -231 (1994b).

ECEPP/2: Momany, F. A., McGuire, R. F., Burgess, A. W., & Scheraga, H. A., (1975) Energy Parameters in Polypeptides VII, Geometric Parameters, Partial Charges, Non-bonded Interactions, Hydrogen Bond Interactions and Intrensic Torsional Potentials for Naturally Ocurring Amino Acids, J. Phys. Chem. 79, 2361-2381. Nemethy, G., Pottle, M. S., & Scheraga, H. A., (1983) Energy Paramters in Polypeptides, 9. Updating of Geometrical Parameters, Non-bonding Interactions and Hydrogen Bonding Interactions for Naturally Occuring Amino Acids, J. PHys. Chem. 87, 1883-1887.

Sippl, M. J., Nemethy, G., & Scheraga, H. A., (1984) Intermolecular Potentials for Crystal Data 6. Determination of Empirical Potentials for 0-H—O=C Hydrogen Bonds for Packing Configurations, J. Phys. Chem. 88, 6231-6633.

GROMOS: Hermans, J., Berendsen, H. J. C., van Gunsteren, W. F., & Postma, J. P. M., (1984) “A Consistent Empirical Potential for Water-Protein Interactions,” Biopolymers 23, 1 Ott, K-H., B. Meyer (1996) “Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations,” J Comp Chem 17, 1068-1084>

van Gunsteren, W. F., X. Daura and A.E. Mark (1997) “The GROMOS force field” in Encyclopaedia of Computational Chemistry ()

MM2: Allinger, N. L. (1977) Conformational Analysis 130. MM2. A Hydrocarbon Force Field Utilizing V1 and V2 Torsional Terms, J. Am. Chem. Soc. 99, 8127-8134. Allinger, N. L., Kok, R. A., and Imam, M. R. (1988) Hydrogen Bonding in MM2, J. Comp. Chem. 9, 591-595.

Lii, J-H., Gallion,S., Bender,C., Wikstrom, H., Allinger, N. L., Flurchick, K. M., and Teeter, M. M.,(1989) Molecular Mechanics (MM2) “Calculations on Peptides and on the Protein Crambin Using the Cyber 205” J. Comp. Chem. 10, 503-513.

MM3: NOTE: In some **s of this series, the MM3 stretch potential is written incorrectly. The proper potential is E = ….(7/12) (2.55(l-lo))2] (J-H. Lii, personal communication). Allinger, N. L., Yuh, Y. H., & Lii, J-H. (1989) Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 1. J. Am. Chem. Soc. 111, 8551-8565.

Hay, B. P., Yang, L., Lii, J-H., and Allinger, N. L. (1998) An extended MM3(96) force field for complexes of the group 1A and 2A cations with ligands bearing conjugated ether donor groups, Theochem: J. Molecular Structure 428, 203-219

Lii, J-H., & Allinger, N. L. (1989a) Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 2. Vibrational Frequencies and Thermodynamics, J. Am. Chem. Soc. 111, 8566-8575.

Lii, J-H., & Allinger, N. L. (1989b) Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 3. The van der Waals Potentials and Crystal data for Aliphatic and Aromatic Hydrocarbons, J. Am. Chem. Soc. 111, 8576-8582.

Lii, J-H., & Allinger, N. L. (1991) The MM3 Force Field for Amides, Polypeptides and Proteins, J. Comp. Chem. 12, 186-199.

Lii, J-H., & Allinger, N. L. (1998) Directional Hydrogen Bonding in the MM3 Force Field. II. J. Comp. Chem. 19, 1001-1016.

MM4: Allinger, N. L., K. Chen, and J-H Lii (1996) “An Improved Force Field (MM4) for Saturated Hydrocarbons,” J. Comp. Chem. 17, 642-668. Allinger, N. L., K. Chen, J. A. Katzenellenbogen, S. R. Wilson and G. M. Anstead (1996) “Hyperconjugative Effects on Carbon-Carbon Bond Lengths in Molecular Mechanics (MM4)” J. Comp. Chem. 17, 747-755.

Allinger, N. L., and Y. Fan (1997) “Molecular Mechanics Studies (MM4) of Sulfides and Mercaptans,” J. Comp. Chem.18, 1827-1847.

Nevens, N., K. Chen and N. L. Allinger (1996) “Molecular Mechanics (MM4) Calculations on Alkenes,” J. Comp. Chem. 17, 669-694.

Nevins, N., J-H. Lii and N.L. Allinger (1996) “Molecular Mechanics (MM4) Calculations on Conjugated Hydrocarbons,” J. Comp. Chem. 17, 695-729.

Nevins, N., and N. L. Allinger (1996) “Molecular Mechanics (MM4) Vibrational Frequency Calculations for Alkenes an Conjugated Hydrocarbons,” J. Comp. Chem. 17, 730-746.

MMFF94: Halgren, T. A. (1992) J. Am. Chem. Soc. 114, 7827-7843. Halgren, T. A. (1996) “Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization and Performance of MMFF94,” J. Comp. Chem 17, 490-519.

Halgren, T. A. (1996) “Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions,” J. Comp. Chem. 17, 520-552.

Halgren, T. A. (1996) “Merck Molecular Force Field. III. Molecular Geometrics and Vibrational Frequencies for MMFF94,” J. Comp. Chem. 17, 553-586.

Halgren, T. A., and Nachbar, R. B. (1996) “Merck Molecular Force Field. IV. Conformational Energies and Geometries,” J. Comp. Chem. 17, 587-615.

Halgren, T. A. (1996) “Merck Molecular Force Field. V. Extension of MMFF94 using Experimental Data, Additional Computational Data and Empirical Rules,” J. Comp. Chem. 17, 616-641.

Tripos: Clark, M., Cramer III, R. D., van Opdenhosch, N., (1989) Validation of the General Purpose Tripose 5.2 Force Field, J. Comp. Chem. 10, 982-1012.

Comparisons and Evaluations: Engler, E. M., J. D. Andose and P. v. R. Schleyer (1973) “Critical Evaluation of Molecular Mechanics,” J. Am. Chem. Soc. 95, 8005-8025. Gundertofte, K., J. Palm, I. Pettersson and A. Stamvik (1991) “A Comparison of Conformational Energies Calculated by Molecular Mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, ChemX) and Semiempirical (AM1 and PM3) Methods,” J. Comp. Chem. 12, 200-208.

Gundertofte, K., T. Liljefors, P-O Norrby, I. Pattesson (1996) “Comparison of Conformational Energies Calculated by Several Molecular Mechanics Methods,” J. Comp. Chem. 17, 429-449 (1996).

Hall, D., and N. Pavitt (1984) “A Appraisal of Molecular Force Fields for the Representation of Polypeptides,” J. Comp. Chem. 5, 441-450.

Hobza, P., M. Kabelac, J. Sponer, P. Mejzlik and J. Vondrasek (1997) “Performance of Empirical Potentials (AMBER, CFF95, CVFF, CHARMM, OPS, POLTEV), Semiemprical Quantum Chemical Methods (AM1, MNDO/M, PM3) and ab initio Hartree-Fock Method for Interaction of DNA Bases: Comparison of Nonempirical Beyond Hartree-Fock Results,” J. Comp. Chem. 18, 1136-1150.

Kini, R. M., and H. J. Evans (1992) “Comparison of Protein Models Minimized by the All-Atom and United Atom Models in the AMBER force Field,” J. Biomol. Structure and Dynamics 10, 265-279.

Roterman, I. K., Gibson, K. D., and Scheraga, H. A. (1989) “A Comparison of the CHARMM, AMBER, and ECEPP/2 Potential for Peptides I.” J. Biomol. Struct. and Dynamics 7, 391-419.

Roterman, I. K., Lambert, M. H., Gibson, K. D., and Scheraga, H. A. (1989) “A Comparison of the CHARMM, AMBER, and ECEPP/2 Potential for Peptides II.” J. Biomol. Struct. and Dynamics 7, 421-452.

Whitlow, M., and M. M. Teeter (1986) “A Empirical Examination of Potential Energy Minimization using the Well-Determined Structure of the Protein Crambin,” J. Am. Chem. Soc. 108, 7163-7172.

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