MM/PBSA: continuum electrostatics calculations of HIV protease inhibitor binding free energies

Nathan Baker

Washington University in St. Louis
Department of Biochemistry and Molecular Biophysics
Center for Computational Biology

David Sept

Washington University in St. Louis
Department of Biomedical Engineering
Center for Computational Biology

Copyright © 2005 by Washington University in St. Louis

Table of Contents

Introduction

MM/PBSA methods
HIV protease and amprenavir

Tips for MM/PBSA calculations

Generating PQR files

Electrostatics and solvation calculations

Polar solvation energies
Coulombic electrostatic energies
Apolar solvation energies

Molecular mechanics energies

Quasi-harmonic entropies

Lab report instructions and questions

List of Equations
1. MM/PBSA binding free energy approximation
2. MM/PBSA binding solvation free energy approximation
3. MM/PBSA binding gas-phase free energy approximation
4. Molecular mechanics contribution to MM/PBSA binding phase free energy approximation
5. Quasi-harmonic entropy approximation (determinant form)
6. Quasi-harmonic entropy approximation (eigenvalue form)

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