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.