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APBS is often used together with the PDB2PQR software; e.g., ,in the following type of workflow
- Start with a PDB ID or locally generated PDB file (see PDB molecular structure format).
- 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¶
- YAML- and JSON-format input files
- Old APBS input format
- Solvation energies
- Binding energies
- Protein-RNA binding linked equilibria
- VIsualization with PyMOL
- Virtual reality with UnityMol
Tests and validation¶
APBS is distributed with testing tools and validation examples.
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.