Using APBS

Note

Before you begin! PDB2PQR funding is dependent on your help for continued development and support. Please register before using the software so we can accurately report the number of users to our funding agencies.

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 has a new input file format that accepts YAML- or JSON- format input. The old APBS input format has been deprecated but will continue to be supported for the next few releases.

New and old input file formats

• YAML- and JSON-format input files
  • Data loading input file section (required)
  • Calculation input file section (required)
  • Results processing section (optional)
  • Input file class structure
• Old APBS input format
  • 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

Tests and validation

APBS is distributed with testing tools and validation examples.

• APBS validation and test cases

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.

Notes on units

APBS and PDB2PQR use a few different sets of units, explained in the following sections:

• Numbers
• Length
• Volume
• Density and concentration
• Temperature
• Charge
• Energy
• Surface tension
• Pressure
• Electrostatic potential