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

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

* `PyMOL <https://pymol.org/>`_
* `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_
* `NGL Viewer <http://nglviewer.org/ngl/>`_
* `Chimera <https://www.cgl.ucsf.edu/chimera/>`_
* `PMV <http://mgltools.scripps.edu/packages/pmv>`_

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Dynamics simulations
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As an example of PDB2PQR and APBS integration with molecular mechanics sofware, the `iAPBS <https://mccammon.ucsd.edu/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 <http://www.ks.uiuc.edu/Research/namd/>`_, `AMBER <http://ambermd.org/>`_, and `CHARMM <https://www.charmm.org/charmm/>`_.

APBS is also used directly by Brownian dynamics software such as `SDA <https://mcm.h-its.org/sda/>`_ and `BrownDye <http://browndye.ucsd.edu/>`_.