.. |GROMACS| raw:: html

   <a href="http://www.gromacs.org/" target="_blank">GROMACS</a>

.. |APBS| raw:: html
   
   <a href="http://www.poissonboltzmann.org/" target="_blank">APBS</a>

.. |g_mmpbsa publication| raw:: html

   <a href="http://pubs.acs.org/doi/abs/10.1021/ci500020m" target="_blank">g_mmpbsa - A GROMACS tool for high-throughput MM-PBSA calculations</a>

.. |APBS publication| raw:: html
   
   <a href="http://www.pnas.org/content/98/18/10037.abstract" target="_blank">Electrostatics of nanosystems: Application to microtubules and the ribosome</a>

.. |SASA publication| raw:: html
   
   <a href="http://onlinelibrary.wiley.com/doi/10.1002/jcc.540160303/abstract" target="_blank">The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies</a>

.. |g_mmpbsa forum| raw:: html

   <a href="https://groups.google.com/d/forum/g_mmpbsa" target="_blank">g_mmpbsa forum</a>

Introduction
=============

g_mmpbsa is developed using two widely used open source software i.e. |GROMACS| and |APBS| and it has similar user interface like other GROMACS tools.
It is now upgraded as Python package for easy installation and usage.

g_mmpbsa contains several `sub-commands <https://g-mmpbsa.readthedocs.io/en/latest/commands/index.html>`_ to carry out binding energy calculation using MM/PBSA method and
energetic contribution of each residue to the binding using energy decomposition scheme.

Now g_mmpbsa can be directly installed on linux using ``python -m pip install g-mmpbsa`` and it supports all GROMACS version above 2018+.

Please **post problems and queries** in |g_mmpbsa forum|, we will try our best to provide the solution.


----

Please always cite following three publications
------------------------------------------------

* Kumari *et al* (2014) |g_mmpbsa publication| *J. Chem. Inf. Model.* 54:1951-1962.

* Baker *et al* (2001) |APBS publication| *Proc. Natl. Acad. Sci. USA*  98:10037-10041.

* Eisenhaber *et al.* (1995) |SASA publication| *J. Comput. Chem.* 16:273-284.


.. toctree::
   :maxdepth: 1
   :caption: Contents

      Download and Installation <install.rst>
      Getting started with MM/PBSA calculation <quick-run.rst>
      g_mmpbsa commands <commands/index>
      Solvation Energy Parameters <parameters/index>
      Tutorials <tutorials/index>
      Change log <ChangeLog.rst>