These are a collection of examples of Poisson-Boltzmann (PB) electrostatics calculations performed using APBS. The purpose of these is to demonstrate the different applications of electrostatics calculations and some common caveats.
All these examples are available as a tarball. To untar this, type:
gzip -dc examples.tar.gz | tar xvf -
and change to the resulting examples directory.
The Born ion is a simple sphere with a point charge and a dielectric constant of 1.0 embedded in a homogeneous medium of arbitrary dielectric. Due to the simple geometry of this system, most electrostatic quantities have analytic formulas. Please see born/index.html for input files and scripts for this example.
Desolvation forces/energies play an important role in electrostatically-driven biological interactions. This example demonstrates the simplest system where desolvation forces can be observed: two Born ions interacting at different distances. Please see ion-pmf/index.html for input files and scripts for this example.
Ligand binding energies are one of the most popular applications of PB calculations; especially in drug design applications. This example demonstrates the calculation of electrostatic contributions to ligand binding for the balanol-protein kinase A system. Please see ligand/index.html for input files and scripts for this example.
Ionic strength affects a variety of thermodynamic and kinetic aspects of biological systems. Of these effects, only a few non-specific interactions can be described with implicit solvent methods such as the PBE. Foremost among these non-specific interactions are screening effects which describe the dampening of electrostatic interactions in the presence of increased salt concetrations. Please see screening/index.html for input files and scripts for this example.
An additional non-specific interaction between ions and biomolecules is often found in DNA systems. Specifically, DNA molecules are known to "condense" a layer of positive charges which screens the majority of their high charge density. Such screening is due both to DNA's charge distribution and its geometry; condensation (as observed in DNA) is not associated with globular biomolecular structures. Please see condensation/index.html for input files and scripts for this example.
More example input files, including protein-protein interactions and force evaluations, are available as part of the APBS distribution.