.. _gmx anadock:

gmx anadock
===========

Synopsis
--------

.. parsed-literal::

    gmx anadock [:strong:`-f` :emphasis:`[<.pdb>]`] [:strong:`-od` :emphasis:`[<.xvg>]`] [:strong:`-of` :emphasis:`[<.xvg>]`] [:strong:`-g` :emphasis:`[<.log>]`]
                [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]free`] [:strong:`-[no]rms`] [:strong:`-cutoff` :emphasis:`<real>`]

Description
-----------

``gmx anadock`` analyses the results of an Autodock run and clusters the
structures together, based on distance or RMSD. The docked energy
and free energy estimates are analysed, and for each cluster the
energy statistics are printed.

An alternative approach to this is to cluster the structures first
using :doc:`gmx cluster <gmx-cluster>` and then sort the clusters on either lowest
energy or average energy.

Options
-------

Options to specify input files:

``-f`` [<.pdb>] (eiwit.pdb)
    Protein data bank file

Options to specify output files:

``-od`` [<.xvg>] (edocked.xvg)
    xvgr/xmgr file
``-of`` [<.xvg>] (efree.xvg)
    xvgr/xmgr file
``-g`` [<.log>] (anadock.log)
    Log file

Other options:

``-xvg`` <enum> (xmgrace)
    xvg plot formatting: xmgrace, xmgr, none
``-[no]free``  (no)
    Use Free energy estimate from autodock for sorting the classes
``-[no]rms``  (yes)
    Cluster on RMS or distance
``-cutoff`` <real> (0.2)
    Maximum RMSD/distance for belonging to the same cluster

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

   More information about |Gromacs| is available at <http://www.gromacs.org/>.