Table of Contents
MOLECULAR MECHANICS
The Molecular Mechanics description of a structure consists of...
Molecular Mechanics Force Field Or Potential Functions
What about the ellipsis, …?
Force fields may be classified by...
A Survey & Comparison of some Force Field Functions
Some Bond Stretch Functions:
However, since bond lengths don’t vary much at room temperature, the fit to bottom of “well” is judged more important and receives more weight.
Comparison of some values:
For example, the CA-C bond length potentials:
Similarly, Bond Angle Functions:
Comparison of some values:
Torsion Angle Functions:
Some other torsion potentials...
NON-BONDING INTERACTIONS
Other combination rules...
Hill potentials, e.g. MM2:
Buffered-14-7 potential (Halgren, 1992)
Hill and Buffered-14-7 potentials are "Softer”, Lennard Jones is “Harder” for the same well depth and equilibrium distance.
Electrostatic interactions
Monopole models...
Multipole models...
with MM2, a dipole-dipole potential:
with MM3, dipole-dipole potential is
retained, but provision is made for interactions
of a formal charge (e.g. -NH3+ groups) by ...
Fixes for Coulombic Potentials
Solvent screening...
Each force field has added functions...
…to fix problems, other geometrical constraints
...To fix problems, other geometrical constraints
...to fix H-bond geometry- added potential
The CHARMM H-bond potential...
...to fix H-bond geometry- added potential
The MM3 h-bond potential...
...to couple bond stretching and angle bending, i.e. off-diagonal terms
Some examples...
Some examples...
…to add chemistry
Adding chemistry...
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Author: John E. Wampler
References:
Molecular Mechanics and Force Field Reference List
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