APBS examples and test cases
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
- 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.
- Input files:
- apbs-mol-auto.in - Sequential, 2-level focusing to <=0.725 A, NPBE, srfm mol
- apbs-smol-auto.in - Sequential, 2-level focusing to <=0.725 A, NPBE, srfm smol
- apbs-mol-parallel.in - Parallel with 8 processors, focusing to ~0.9 A, LPBE, srfm mol
- apbs-smol-parallel.in - Parallel with 8 processors, focusing to ~0.9 A, LPBE, srfm smol
Born Ion
- README
- Source: Nathan Baker
- Description: Calculate solvation energies for ions of various sizes and
compare to the analytical results.
- Input files:
FKBP
- README
- Source: Jung-Hsin Lin
- Description: Binding of various (small) ligands to FKBP. Analogous to
HCA binding case (except it works).
- Input files:
- 1d7h-dmso/apbs-mol.in - 1d7h-dmso, 2-level focusing to 0.225 A, VdW surface, srfm mol
- 1d7h-dmso/apbs-smol.in - 1d7h-dmso, 2-level focusing to 0.225 A, VdW surface, srfm smol
- 1d7i-dss/apbs-mol.in - 1d7i-dss, 2-level focusing to 0.225 A, VdW surface, srfm mol
- 1d7i-dss/apbs-smol.in - 1d7i-dss, 2-level focusing to 0.225 A, VdW surface, srfm smol
hca-bind
- README
- Source: UHBD
- Description: Calculate the binding of a small molecule (acetazolamide)
to a medium-sized protein (human carbonic anhydrase).
- Input files:
- apbs-mol.in - 2-level focusing to 0.225 A, VdW surface, srfm mol
- apbs-smol.in - 2-level focusing to 0.225 A, VdW surface, srfm smol
ionize
- README
- Source: UHBD
- Description: Calculate electrostatic contributions to the ionization
energy of acetic acid.
- Input files:
ion-protein
- README
- Source: Dave Sept
- Description: Calculate energy of placing an ion near a macromolecule
- Input files:
pka-lig
- README
- Source: Chung Wong
- Description: Calculate binding energies of a ligand to protein kinase A.
- Input files:
- apbs-mol-vdw.in - 2-level focusing to 0.250 A spacing, VdW surface, srfm mol
- apbs-smol-vdw.in - 2-level focusing to 0.250 A spacing, VdW surface, srfm smol
- apbs-mol-surf.in - 2-level focusing to 0.250 A spacing, molecular surface, srfm mol
- apbs-smol-surf.in - 2-level focusing to 0.250 A spacing, molecular surface, srfm smol
point-pmf
- README
- Source: Nathan Baker
- Description: See how well we do reproducing Coulomb's law.
- Input files:
- apbs.in - Focusing to 0.21 A, srfm spl2
solv
- README
- Source: UHBD
- Description: Calculate the solvation energies of methanol and methoxide.
- Input files: