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==========
Using APBS
==========
.. _PDB ID: https://www.rcsb.org/pages/help/advancedsearch/pdbIDs
.. note::
*Before you begin!* PDB2PQR funding is dependent on your help for continued development and support. Please `register <http://eepurl.com/by4eQr>`_ 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 <https://github.com/Electrostatics/pdb2pqr>`_; e.g., ,in the following type of workflow
#. Start with a `PDB ID`_ or locally generated PDB file (see :doc:`/formats/pdb`).
#. Assign titration states and parameters with :program:`pdb2pqr` to convert the protein and ligands to PQR format (see :doc:`/formats/pqr`).
#. Perform electrostatics calculations with :program:`apbs` (can be done from within the `PDB2PQR web server <web-server>`_).
#. Visualize results from within PDB2PQR web server or with :ref:`other-software`.
--------------
Web server use
--------------
Most users will use PDB2PQR through `the web server <http://server.poissonboltzmann.org/>`_ (after `registering <http://eepurl.com/by4eQr>`_, of course).
However, it is also possible to install local versions of PDB2PQR and run these through the command line.
----------------
Command line use
----------------
.. code-block:: bash
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 :ref:`new input file format <new_input_format>` that accepts `YAML- <http://yaml.org>`_ or `JSON- <http://json.org>`_ format input.
The :ref:`old APBS input format <old_input_format>` has been deprecated but will continue to be supported for the next few releases.
.. toctree::
:maxdepth: 2
:caption: New and old input file formats
input/new/index
input/old/index
.. _examples:
--------
Examples
--------
.. _PDB2PQR: https://github.com/Electrostatics/pdb2pqr
.. _APBS-PDB2PQR web interface: http://server.poissonboltzmann.org/
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.
.. toctree::
:maxdepth: 2
examples/solvation-energies
examples/binding-energies
examples/salt-linkage
examples/visualization-pymol
examples/visualization-unitymol
--------------------
Tests and validation
--------------------
APBS is distributed with testing tools and validation examples.
.. toctree::
:maxdepth: 1
tests
-------------------
Tools and utilities
-------------------
APBS is distributed with utilities designed to simplify typical tasks associated with electrostatics calculations.
.. toctree::
:maxdepth: 1
tools
.. _other-software:
--------------
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 <https://pymol.org/>`_
* `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_
* `Chimera <https://www.cgl.ucsf.edu/chimera/>`_
* `PMV <http://mgltools.scripps.edu/packages/pmv>`_
^^^^^^^^^^^^^^^^^^^^
Dynamics simulations
^^^^^^^^^^^^^^^^^^^^
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/>`_.
--------------
Notes on units
--------------
APBS and PDB2PQR use a few different sets of units, explained in the following sections:
.. toctree::
:maxdepth: 2
units
|
