Poisson Boltzmann Tutorial
Using APBS for implicit solvent calculations

Table of Contents
Introduction to PB solvers
APBS hardware considerations
Running APBS on the CTBP cluster
Calculation setup
PQR files
Input parameters
Visualizing electrostatic potentials
FKBP - 4 hydroxy butanone
Visualization with VMD
Solvation energy calculation
Calculation input
Accounting for self-energies
Binding energy calculation
Parallel processor speedup

Introduction

There are several programs available for PB calculations:

This tutorial introduces the Adaptive Poisson-Boltzmann Solver (APBS http://agave.wustl.edu/apbs/), which is open source software for the numerical solution of the Poisson-Boltzmann partial differential equation, which models the electrostatic potential of charges in an ionic solution at equilibrium. This implicit representation of the solvent environment and solvation effects can be used to study molecular systems in multiple ways. We will demonstrate three of the most common uses including the qualitative assessment of the electrostatic potential surrounding a biomolecule and two quantitative calculations of solvation and binding free energies.

Note that a more extensive tutorial is available at http://agave.wustl.edu/apbs/doc/html/tutorial/index.html

APBS Hardware Considerations

Electrostatic calculations with APBS are not usually CPU intensive, an average APBS calculation runs for a couple of minutes. However, since the PB equation is solved numerically on a grid, all grid points must be held in the system memory (RAM) for the calculation to be efficient. Amount of available RAM is thus the calculation bottleneck. This is not very important when running small systems since most modern computers have at least 400MB of RAM available but this becomes crucial when studying large systems or using high resolution grids. To avoid or minimize this bottleneck APBS uses approach called parallel focusing method. The numerical grid which envelopes the molecule is basically divided up to number of smaller grids which are then solved independently on one or more processors.

Running APBS on the CTBP cluster

Log in to the cluster and setup APBS environment:


ssh -X username@ctbp1.ucsd.edu
source /soft/linux/etc/setup_apbs

To copy and untar all tutorial example files to your home directory:


cd
mkdir PBTutorial
cd PBTutorial
cp /soft/linux/src/Workshop/* .
ls *tar | xargs -l1 tar xvf

All computationally intensive jobs on the cluster must be run through the queuing system which distributes jobs to the computational nodes. For examples in this tutorial which do not use multiple CPUs (all except the parallel job example) type qrsh which will assign you a computational node for interactive use. To end this interactive node use simply type exit and you will be returned to the frontend (ctbp1.ucsd.edu) prompt. Note: Don't forget to source /soft/linux/etc/setup_apbs after you logged in to the computational node to set up your APBS environment.

When running the parallel example you must submit your job from the frontend using qsub command (see the parallel example page). Instruction for the queuing system about your job requirements (how many processors you are requesting, how much memory, how much time, etc.) are specified in an SGE script file (.sge) which you have to create first. Examples of SGE files are included in all APBS tutorials.

Important links:

Acknowledgment: Much of the material in this tutorial was modified from the APBS tutorial created by Nathan Baker.
Authors: Jessica Swanson, Robert Konecny and the McCammon Group - UCSD
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Calculation setup