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g_anadock

g_anadock(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_anadock(1)

NAME

       g_anadock - cluster structures from Autodock runs

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_anadock  -f  eiwit.pdb  -ox  cluster.pdb  -od	edocked.xvg -of efree.xvg -g anadock.log -[no]h -[no]version -nice int -xvg enum -[no]free
       -[no]rms -cutoff real

DESCRIPTION

	g_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  g_cluster and then sort the clusters on either lowest energy or
       average energy.

FILES

       -f eiwit.pdb Input
	Protein data bank file

       -ox cluster.pdb Output
	Protein data bank file

       -od edocked.xvg Output
	xvgr/xmgr file

       -of efree.xvg Output
	xvgr/xmgr file

       -g anadock.log Output
	Log file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[no]freeno
	Use Free energy estimate from autodock for sorting the classes

       -[no]rmsyes
	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.gromacs.org/>.

								  Mon 4 Apr 2011						      g_anadock(1)