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APBS is often used together with the PDB2PQR software; e.g., ,in the following type of workflow
Assign titration states and parameters with pdb2pqr to convert the protein and ligands to PQR format (see PQR molecular structure format).
Perform electrostatics calculations with apbs (can be done from within the PDB2PQR web server).
Visualize results from within PDB2PQR web server or with Other software.
Web server use¶
Command line use¶
apbs [options] input-file
where the list of
[options] can be obtained by running APBS with the
The input file format is described below.
Input file syntax¶
APBS input files are loosely-formatted files which contain information about the input, parameters, and output for each calculation.
These files are whitespace- or linefeed-delimited.
Comments can be added to the input files via the
# character; all text between the
# and the end of the line is not parsed by APBS.
If pathnames used in the input file contain spaces, then the entire pathname must be enclosed in quotes.
For example, if you wanted to refer to the file
foo which resides in a directory with spaces in its name, then you should refer to
"/path with spaces/foo".
Specific examples of APBS input are provided in Examples.
APBS input files contain three basic sections which can be repeated any number of times:
- READ input file section
section for specifying input
- ELEC input file section
section for specifying polar solvation (electrostatics) calculation parameters
- APOLAR input file section
section for specifying apolar solvation calculation parameters
- PRINT input file section
section for specifying summary output
The APBS input file is constructed from these sections in the following format:
READ ... END ELEC ... END APOLAR ... END PRINT ... END QUIT
These sections can occur in any order and can be repeated any number of times. However, the sections are inter-dependent. For example, PRINT requires ELEC and/or APOLAR while ELEC requires one or more READ sections. Sections can also be repeated; several READ statements may be used to load molecules and multiple ELEC or APOLAR sections would specify various electrostatics calculations on one or more molecules.
Each section has the following syntax:
SECTION [name <id>]
where the optional
name argument allows the user to include a string to identify the section.
In the absence of this argument, sections are assigned numerical IDs.
- Solvation energies
- Binding energies
- Protein-RNA binding linked equilibria
- VIsualization with PyMOL
- Virtual reality with UnityMol
Tools and utilities¶
APBS is distributed with utilities designed to simplify typical tasks associated with electrostatics calculations.
A variety of other software can be used to visualize and process the results of PDB2PQR and APBS calculations.
Examples of visualization software that work with output from PDB2PQR and APBS:
As an example of PDB2PQR and APBS integration with molecular mechanics sofware, the iAPBS library was developed to facilitate the integration of APBS with other molecular simulation packages. This library has enabled the integration of APBS with several molecular dynamics packages, including NAMD, AMBER, and CHARMM.