APBS: Adaptive Poisson-Boltzmann Solver

Software for evaluating the electrostatic properties of nanoscale biomolecular systems

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.

This software was written by Nathan Baker in collaboration with J. Andrew McCammon and Michael Holst. APBS has been enhanced by contributions from several other authors (see documentation).

APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries written in an object-oriented version of C. It is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at <http://www.FEtk.ORG>.

Please visit the following links for more information about APBS:

• Documentation
• Download/Availability
• Mailing lists
• Supporting organizations
• License
• NBCR APBS Quick Facts Brochure
• PDB2PQR web server
• APBS web portals: version 0.4.0 via Gemstone, current version

Supporting Organizations

• National Institutes of Health (funding via grant GM069702-01)
• National Biomedical Computation Resource (computer resources and deployment)
• Washington University School of Medicine (funding)
• National Partnership for Advanced Computational Infrastructure (funding and computer resources)

Availability

Please acknowledge your use of APBS by citing:

• Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. (Link)

Additional articles discussing APBS and the PBE are available from the Baker group website.

Please acknowledge your use of the Holst group software by citing:

• M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993.
• M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem. 16, 337-364, 1995.

for PMG (the multigrid solver) or

• M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics 15, 139-191, 2001. (Link).
• R. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Review 45, 291-323, 2003. (Link).

for FEtk (the finite element solver).

Download

The most recent version of APBS can be obtained in source code and binary forms here: http://agave.wustl.edu/apbs/download.

Additionally, the APBS archive is available on the web for browsing.

Mailing Lists

There are two mailing lists associated with the APBS software:

• apbs-announce: A low-traffic list for announcements regarding bugs and new versions of the software:
  List web page
  List archives
• apbs-users: A list for discussion of APBS, troubleshooting, and reporting potential bugs:
  List web page
  List archives