Table of Contents
Parameters for Molecular Mechanics
Parameter optimization
Parameter optimization...
Parameter optimization… What goal?
Parameter optimization...
Parameter optimization...
General Principles and Issues
Remember: Goal is parameters that “fit in” to the force field.
Therefore: We must understand where the built-in parameters
of that particular force field came from.
General Principles & Issues...
Some Recipes
Parameters based on other parameters
Extrapolating based on bond-lengths comes from correlation between Lengths, bond order and force constants:
AMBER Parmeters taken from MM3
However, the resulting parameters correlate well with existing ones.
Parameters based on experimental data
Transfer force parameters from analysis of vibrational spectra
Fit non-bonded parameters to simulate pure fluid properties
OPLS non-bonded potential between atoms i and j:
Comparison of non-bonded parameters*:
Extract equilibrium parameters from known structures.
HOWEVER...
Fit parameters to give experimental geometries
Parameters from theoretical calculations
Direct evaluation of individual potentials
Direct evaluation…Bond stretch parameters
High level ab initio bond lengths vs experimental
Example, Morse potential fit to the formaldehyde carbonyl stretch*
What about a harmonic fit to this data?
Example cont., harmonic fit to the H-C-H bending of formaldehyde*
Closer look… Formaldehyde
Direct evaluation...
Force constants for bond stretch:
Matching Calculated Data sets
II. Step-Wise Approach (Hopfinger & Pearlstein, 1984):
Step wise...
Matching Calculated Data sets...
III. Global Approach (Cannon, 1993).
Hybrid parameters sets
Hybrid parameters sets…
Norrby & Liljefors (1998)...
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Author: J. E. Wampler
References:
General Reference and References Cited (alphabetical):
NOTE: References for AMBER, CHARMm, MM3 and OPLS parameters are given separately below
Bowen, J. P., and N. L. Allinger (1991) in Review of Computational Chemistry 1 (K. Lipkowitz, ed.) pp. 81-97.
Cannon, J. F. (1993), J. Comp. Chem. 14, 995-1005.
Comba, P., and Hambley, T. W. (1995) Molecular Modeling of Inorganic Compounds, VCH, Weinheim, Germany.
Hay, B. P. (1993) Methods for molecular mechanics modeling of coordination compounds, Coord. Chem. Rev. 126, 177-236.
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,
Hopfinger, A. J. & R. A. Pearlstein (1994), J. Comp. Chem. 5, 486-499.
Leach, A. R. (1996) Molecular Modeling Principles and Applications, Addison Wesley, Longman Limited, Essex, England
Liang, G. Y., Fox, P. C., and Bowen, J. P. (1996) Parameter Analysis and
refinement toolkit system and its application in MM3 parameterization for
Phosphine and its derivatives, J. Comp. Chem. 17, 940-953.
Norrby, P-O., and Liljefors, T. (1998) Automated molecular mechanics
parameterization with simultaneous utilization of experimental and quantum
mechanical data, J. Comp. Chem. 19, 1146-1166.
Orozco, M., & Luque, F. J., (1993), J. Comp. Chem. 14, 881-894.
Palma, P. N. L. (1998), "Studies of Macromolecular Recognition and Prediction of Redox Properties of Metalloproteins," Doctoral Dissertation, Universidade Nova de Lisboa, Portugal.
Schnur, D. M., M. V. Grieshaber and J. P. Bowen (1991), J. Comp. Chem. 12, 844-849.
OPLS Parameters:
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.
Developement of MM3 Parameters:
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.
Development of AMBER Parameters:
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.
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.
CHARMm Paramters:
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy, minmimization, and dynamics calculations. J. Comp. Chem. (1983) 4, 187-217.
Momany, F. A., & Rone, R., (1992) Validation of the General Purpose QUANTA 3.2/CHARMm Force Field, J. Comp. Chem. 13, 888-900.
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