gmx-anadock man page on DragonFly

gmx-anadock man page on DragonFly

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gmx-anadock(1)			GROMACS Manual			gmx-anadock(1)

NAME
       gmx-anadock - Cluster structures from Autodock runs

SYNOPSIS
       gmx anadock [-f [<.pdb>]] [-od [<.xvg>]] [-of [<.xvg>]]
		   [-g [<.log>]] [-nice <int>] [-xvg <enum>] [-[no]free]
		   [-[no]rms] [-cutoff <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 gmx cluster and then sort the clusters on either lowest energy or
       average energy.

OPTIONS
       Options to specify input and output files:

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

       -od [<.xvg>] (edocked.xvg) (Output)
	   xvgr/xmgr file

       -of [<.xvg>] (efree.xvg) (Output)
	   xvgr/xmgr file

       -g [<.log>] (anadock.log) (Output)
	   Log file

       Other options:

       -nice <int> (0)
	   Set the nicelevel

       -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
       gromacs(7)

       More  information  about	 GROMACS  is  available	 at   <http://www.gro‐
       macs.org/>.

VERSION 5.0.6							gmx-anadock(1)

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