APBS 0.4.0 User Guide

Adaptive Poisson-Boltzmann Solver

Nathan A Baker

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

Copyright © 2002, 2003, 2004, 2005 by Washington University in St. Louis

Table of Contents
Introduction
Installation
Availability
Binary installation
Source installation
Prerequisites
Preparation for installation
Configuring, compiling, and installing
Machine-specific notes
Overview
Invocation
Other tools
Parameterization
Problem setup
Output data processing
Data visualization
Solvent accessibility
Coulomb's Law and Generalized Born calculations
Eigenvalue analysis
Python development tools
Examples and tutorial
Documentation
Source code
Using APBS
Invocation
Input files
READ statements
ELEC statements
PRINT statements
Using APBS with other programs
Graphical user interfaces
Simulation software
Visualization software
Getting help
User Forums
Mailing Lists
Bug and other problems
Programming
File formats
PQR biomolecular structure format
Parameter file format
Harwell-Boeing column-compressed matrix format
OpenDX scalar data format
Multigrid
Finite element
License
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