NAME
anadock - cluster structures from Autodock runs
VERSION 4.0.1
SYNOPSIS
anadock -f eiwit.pdb -ox cluster.pdb -od edocked.xvg -of efree.xvg -g
anadock.log -[no]h -nice int -[no]xvgr -[no]free -[no]rms -cutoff real
DESCRIPTION
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
-nice int 0
Set the nicelevel
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[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/>.
Thu 16 Oct 2008 anadock(1)