Using APBS

Note

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APBS is often used together with the PDB2PQR software; e.g., ,in the following type of workflow

1. Start with a PDB ID or locally generated PDB file (see PDB molecular structure format).
2. Assign titration states and parameters with pdb2pqr to convert the protein and ligands to PQR format (see PQR molecular structure format).
3. Perform electrostatics calculations with apbs (can be done from within the PDB2PQR web server).
4. Visualize results from within PDB2PQR web server or with Other software.

Web server use

Most users will use PDB2PQR through the web server (after registering, of course). However, it is also possible to install local versions of PDB2PQR and run these through the command line.

Command line use

apbs [options] input-file

where the list of [options] can be obtained by running APBS with the --help option. 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 foo as "/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.

Input file sections

• READ input file section
• ELEC input file section
• APOLAR input file section
• PRINT input file section

Examples

APBS examples start with a PQR file (e.g., generated by PDB2PQR). Some of these examples can be performed through the APBS-PDB2PQR web interface but most require a command-line APBS program.

• Solvation energies
  • Polar solvation
  • Apolar solvation
• Binding energies
  • Free energy cycle
  • Binding energy calculations
• Protein-RNA binding linked equilibria
  • Introduction
  • APBS implementation
  • Automation with Python
  • Visualization
• VIsualization with PyMOL
  • Run the APBS calculation
  • Visualize the results
• Virtual reality with UnityMol
  • Getting the software
  • Using the software

Tools and utilities

APBS is distributed with utilities designed to simplify typical tasks associated with electrostatics calculations.

• Conversion utilities
• Benchmarking utilities
• Setup and analysis utilities

Other software

A variety of other software can be used to visualize and process the results of PDB2PQR and APBS calculations.

Visualization software

Examples of visualization software that work with output from PDB2PQR and APBS:

• PyMOL
• VMD
• Chimera
• PMV

Dynamics simulations

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.

APBS is also used directly by Brownian dynamics software such as SDA and BrownDye.