# APBS examples and test cases

$Id$

This directory serves as the root directory for the APBS test suite. In each directory you will find example input files to use with APBS and a README file displaying the results for different versions of APBS.

Executing `make test` in each directory will run the examples for that directory and log the results to `TESTRESULTS.log`. Executing `make test` from the root examples directory will run all the tests listed below. Tests will either pass, pass with rounding error (within 1E-9 of the expected result), or fail outright.

- Actin dimer (actin-dimer)
  - README
  - Source: Dave Sept
  - Description: Calculate binding energies for actin dimers. This is an example of a large biomolecule binding energy calculation that often requires parallel focusing.
- Alkane nonpolar solvation energies (alkanes)
  - README
  - Source: Nathan Baker, Jason Wagoner
  - Description: Calculate nonpolar solvation energies for various alkanes. Taken from Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-8336, 2006. (http://dx.doi.org/10.1073/pnas.0600118103)
- Born ion (born)
  - README
  - Source: Nathan Baker
  - Description: Calculate solvation energies for ions of various sizes and compare to the analytical results.
- FKBP (FKBP)
  - README
  - Source: Jung-Hsin Lin
  - Description: Binding of various (small) ligands to FKBP. Analogous to HCA binding case (except it works).
- HCA ligand binding (hca-bind)
  - README
  - Source: UHBD
  - Description: Calculate the binding of a small molecule (acetazolamide) to a medium-sized protein (human carbonic anhydrase).
- Acetic acid ionization (ionize)
  - README
  - Source: UHBD
  - Description: Calculate electrostatic contributions to the ionization energy of acetic acid.
- Ion-ion PMF (ion-pmf)
  - README
  - Source: Nathan Baker
  - Description: Calculate solvation energies and solvation force components for ion pairs.
- Ion-protein interaction energies (ion-protein)
  - README
  - Source: Dave Sept
  - Description: Calculate polar energy of placing an ion near a macromolecule
- PKA-balanol binding (pka-lig)
  - README
  - Source: Chung Wong
  - Description: Calculate binding energies of a ligand to protein kinase A.
- Coulomb's law (point-pmf)
  - README
  - Source: Nathan Baker
  - Description: See how well we do reproducing Coulomb's law.
- Methanol solvation (solv)
  - README
  - Source: UHBD
  - Description: Calculate the solvation energies of methanol and methoxide.
- Protein-RNA interactions (protein-rna)
  - README
  - Source: David Draper
  - Description: Calculate the salt dependence of protein interactions with box B RNA hairpin.