Table of Contents
ISSUES OF PROTEIN MOLECULAR MECHANICS
The Atom-type Problem
AMBER Atom types
Is this approach justified... ...and Bond Angles:
Restricted Bond Stretch Description
..more on bond stretch
United atom versus All atom
Is the H-bond a special case? Angle dependence of C=O...H H-bond
Point Charge Model & Point Charges
Types of non-bonded interactions
With polarizable charge centers:
Electrostatic Potential Charges
With good basis set, ab initio calculations predict dipole moments accurately.
Point charges calculated from ab initio results, different types of “charges” represent the dipole with different degrees of accuracy
PROBLEMS WITH FIXED VALUE POINT CHARGES USED TO EVALUATE ELECTROSTATIC POTENTIAL:
DEFENSE OF FIXED VALUES:
Water Models
Some Rigid Water Models
Geometry and Parameters of Some Water Models (selected).
The Three Site TIP3P Performs well
Parameters (focus on AMBER)
some comments
Assign vdW's
OPLS non-bondeds
Comparison of non-bonded parameters
Evaluate ESP charges
Comparison of linear correlation...
Assign equilibrium values
Evaluate force constants..
High level ab initio bond lengths vs experimental
Force constants for bond stretch
Correlation between Lengths and Force constants
The Hybrid approach
The Step-Wise Approach (Hopfinger & Pearlstein, 1984)
Evaluate Bond angle parameters...
The Global Approach (Cannon, 1993)
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