This section gives an overview of the binaries, tools, etc. distributed as part of the APBS software package. It is organized by directory; later chapters provide a more in-depth description on tools specific to particular applications.
Installation and availability section, the main APBS binary, as well as our new Opal client, is installed in
APBS contains a number of tools to facilitate the preparation of APBS runs and analysis of the results.
Note In addition to the tools provided with APBS, there are a number of other programs that are not distributed with APBS but which interoperate with our code. Please see the Running APBS section of this manual for more information.
APBS software. The PDB2PQR service was developed to address these issues. Additionally, APBS provides the ability to read plain PDB-format files and assign charges and radii from user-supplied parameter files. These features are described in the READ parm command description.
APBS provides a few other miscellaneous tools for converting and parameterizing structures:
In addition to parametrization of the molecule, there are several common operations which are performed to setup the calculation. This section reviews some of the tools available for these operations. Please note that PDB2PQR service also prepares APBS input files.
The following scripts help generate or transform APBS input files:
The following tools perform typical analyses of the output data, usually in OpenDX format. These scripts are not meant to be comprehensive; instead, they provide templates for users to generate their own tools.
The following utilities convert APBS grid output (e.g., potentials, accessibility functions, etc.) into a variety of other formats:
The following utilities process APBS grid output in a variety of ways:
This section describes the data visualization tools provided with APBS. A more complete discussion of the various ways to visualize APBS output is presented in the Visualization section of this manual. Old tools for VMD have been removed since they are now completely replaced by OpenDX and APBS functionality available within VMD.
The main APBS executable calculates molecular volumes, surface areas, and other surface-based properties from PQR-format structural data. Such calculations are often used to determine apolar solvation contributions to binding events, etc. See the new APOLAR input file section for more documentation on this APBS feature. With the introduction of this new feature, we have deprecated and removed the stand-alone tools which used to perform these functions.
These utilities are provided for occasional use and are definitely not optimized for speed.
The program tools/manip/coulomb calculates vacuum Coulomb law energies from a PQR file. It has a number of options which can be viewed by running the coulomb program with no arguments.
The program tools/manip/born is a crude, non-optimal, buggy program for calculating Generalized Born electrostatic energies. This is only intended for hacking and general comparison with Poisson-Boltzmann results.
The Python-based program tools/python/runGB.py is a test program designed to calculate generalized Born radii from APBS Poisson-Boltzmann calculations following the general methods of
Onufriev A, Case DA, Bashford D. Effective Born radii in the generalized Born approximation: The importance of being perfect. J Comput Chem, 23 (14), 1297-304, 2002. http://dx.doi.org/10.1002/jcc.10126.
More information on this program can be obtained by running it from the command line with the --help option.
The Python-based program tools/python/readGB.py is a test program designed to use radii calculated from runGB.py (see above) and print out solvation energies. More information on this program can be obtained by running it from the command line with the --help option.
Both of these Python-based programs were written by Justin Xiang.
There are a number of example Python tools and wrappers provided in the tools/python directory. These tools all make use of the APBS SWIG wrappers developed by Todd Dolinsky, Nathan Baker, Alex Gillet, and Michel Sanner. The SWIG wrappers are compiled by default during normal installation. The Python scripts which link to the wrappers (and thereby illustrate their use) include:
The APBS sub-directory examples contains several test systems which show how to use APBS for binding energy, solvation energy, and force calculations. The file examples/README.html contains descriptions of the test cases and links to anticipated results. Examples can be run and compared to expected results by running make test in each example directory.
Additional examples are provided as part of the APBS tutorial (doc/html/tutorial/), described in more detail in the Documentation section.