anadock1
Cluster structures from autodock runs version 4.0.1
Usage
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
Overview
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
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
Releases
3 releases since Debian 4.0 (Etch); the text changed 2 times.