Lab 2
Binding free energies
Nathan Baker
Washington University in St. Louis
Department of Biochemistry and Molecular Biophysics
Center for Computational Biology
Copyright © 2005 by Washington University in St. Louis
Table of Contents
Introduction
Acknowledgments
"Single-point" implicit solvent binding energies
Parameterization
Calculating electrostatic solvation energies
Calculating electrostatic binding energies
Energies by thermodynamic integration
Preparing the Na
+
-ether complex
Loading the parameters and starting structure
Fixing the starting structure
Adding the Na
+
Specifying the perturbation
Solvate
Save your work
Minimization
Thermodynamic integration
λ = 0
λ = 0.25
λ = 0.5, 0.75, 1.00
Performing the integration
MM/PBSA binding energy calculations
Running the trajectories
Na
+
-bound trajectory
K
+
-bound trajectory
Molecular mechanics trajectory analysis
Quasi-harmonic entropy analysis
Energy analysis
Solvation energies
Nonpolar energies
Polar energies
Putting it all together
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Introduction