APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:

• simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics,
• implicit solvent molecular dynamics of biomolecules ,
• solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design,
• and biomolecular titration studies.

APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms.

Create a batch input file, e.g. 'apbs_run', which uses the input file 'apbs.in'. For example:

#!/bin/bash
#PBS -N apbs
#PBS -e apbs.err
#PBS -o apbs.log

cd $PBS_O_WORKDIR
/usr/local/bin/apbs < apbs.in > apbs.in

Submit this job using the PBS 'qsub' command.

qsub -l nodes=1 myscript

See here for more information about PBS. Example input files and expected output can be found in the directory /usr/local/APBS/examples.

Version

APBS v. 0.5.0, using MALOC libraries v. 0.1.2.

Examples

See the APBS example suite The input files are available in /usr/local/apbs/examples.

• Main web site: http://apbs.sourceforge.net/
• Documentation and tutorial: http://apbs.sourceforge.net/doc/index.html
• APBS Users Mailing List: http://lists.sourceforge.net/lists/listinfo/apbs-users - an excellent resource for detailed discussions of the software