gmx-anadock man page

gmx-anadock — Cluster structures from Autodock runs


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


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 gmx cluster and then sort the clusters on either lowest energy or average energy.


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

See Also


More information about GROMACS is available at <>.

Referenced By


Mar 13, 2017 2016.3 GROMACS