Compiling adaptive Poisson-Boltzmann Solver (APBS) on CentOS 5

Adaptive Poisson-Boltzmann Solver (APBS) is a software package for modeling biomolecular solvation through 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.

Installation is very simple. There are many binaries there and you can use the binaries directly. Do note that the latest binaries (apbs-1.3) uses will require glibc 2.7 and greater. If you are using CentOS 5, you may want to use apbs-1.21 binaries or below.

I’m assuming you are using Intel Compilers. You can download and install Intel Compiler.

  1. If you are eligible for the Intel Compiler Free Download. Download the Free Non-Commercial Intel Compiler Download
  2. Build OpenMPI with Intel Compiler

If you are prepared to compile from source using the latest version, then you should be able to use the latest version even on CentOS 5.

To compile from source. The simplest and most straightforward compilation

# tar -zxvf apbs-1.3-source.tar.gz
# cd apbs-1.3-source
# ./configure --prefix=/usr/local/apbs-1.3
# make; make install

To enable openmpi

# ./configure --prefix=/usr/local/apbs-1.3 --with-openmpi=/usr/local/mpi
# make; make install

For more information, do look at the $HOME/apbs-1.3/configure –help or INSTALL file

1. APBS Project Site (