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.