g_anadock

Main Table of Contents

VERSION 4.5
Thu 26 Aug 2010


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

optionfilenametypedescription
-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

optiontypedefaultdescription
-[no]h gmx_bool no Print help info and quit
-[no]version gmx_bool no Print version info and quit
-nice int 0 Set the nicelevel
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]free gmx_bool no Use Free energy estimate from autodock for sorting the classes
-[no]rms gmx_bool yes Cluster on RMS or distance
-cutoff real 0.2 Maximum RMSD/distance for belonging to the same cluster


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