WHAT IS MOLECULAR MECHANICS

Table of Contents

WHAT IS MOLECULAR MECHANICS

The Molecular Mechanics description of a structure consists of...

Molecular Mechanics Force Field Or Potential Functions

A Survey & Comparison of some Force Field Functions

Some Bond Stretch Functions:

Model bond as spring...

Harmonic (AMBER) is simplest function,...

However, since bond lengths don’t vary much ...

Similarly, Bond Angle Functions:

Torsion Angle Functions:

AMBER torsion.

Some other torsion potentials...

NON-BONDING INTERACTIONS

MM2:

Parameters for "Soft" and "Hard" vdW potentials are typically very different

Electrostatic interactions.

NOTE:...

Solvent "screening"..

with MM2 a dipole-dipole potential:

Each force field has added functions...

To fix problems, other geometrical constraints

Hydrogen Bonding.

AMBER H-bond functions

Molecular mechanics minimization.

Molecular dynamics 

Email: wampler@bchiris.bmb.uga.edu

Home Page: http://bmbiris.bmb.uga.edu/wampler

References:

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.

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.

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.

Burkert, U., & Allinger, N. L. (1982) Molecular Mechanics, American Chemical Society, Washington, DC.

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.

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.

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.