Table of Contents
{1} MOLECULAR MECHANICS
{2} The Molecular Mechanics description of a structure consists of...
{3} Molecular Mechanics Force Field Or Potential Functions
{4} What about the ellipsis, …?
{5} Force fields may be classified by...
{6} A Survey & Comparison of some Force Field Functions
{7} Some Bond Stretch Functions:
{8} 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.
{9} Comparison of some values:
{10} For example, the CA-C bond length potentials:
{11} Similarly, Bond Angle Functions:
{12} Comparison of some values:
{13} Torsion Angle Functions:
{14} Some other torsion potentials...
{15} NON-BONDING INTERACTIONS
{16} Other combination rules...
{17} Hill potentials, e.g. MM2:
{18} Buffered-14-7 potential (Halgren, 1992)
{19} Hill and Buffered-14-7 potentials are "Softer”, Lennard Jones is “Harder” for the same well depth and equilibrium distance.
{20} Electrostatic interactions
{21} Monopole models...
{22} Multipole models...
{23} with MM2, a dipole-dipole potential:
{24} with MM3, dipole-dipole potential is
retained, but provision is made for interactions
of a formal charge (e.g. -NH3+ groups) by ...
{25} Fixes for Coulombic Potentials
{26} Solvent screening...
{27} Each force field has added functions...
{28} …to fix problems, other geometrical constraints
{29} ...To fix problems, other geometrical constraints
{30} ...to fix H-bond geometry- added potential
{31} The CHARMM H-bond potential...
{32} ...to fix H-bond geometry- added potential
{33} The MM3 h-bond potential...
{34} ...to couple bond stretching and angle bending, i.e. off-diagonal terms
{35} Some examples...
{36} Some examples...
{37} …to add chemistry
{38} Adding chemistry...
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Author: John E. Wampler
Email: wampler@bchiris.bmb.uga.edu
Home Page: http://bmbiris.bmb.uga.edu/BMB8200
References:
InsightII chapter on Force Fields (MGL copy)
Molecular Mechanics and Force Field Reference List
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