anadock − cluster structures from Autodock runs
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
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.
-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
-[no]h no
Print help info and quit
-nice int 0
Set the nicelevel
-[no]xvgr yes
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-[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
More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.