This is the command gmx-anadock that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-anadock - Cluster structures from Autodock runs
SYNOPSIS
gmx anadock [-f [<.pdb>]] [-od [<.xvg>]] [-of [<.xvg>]] [-g [<.log>]]
[-xvg <enum>] [-[no]free] [-[no]rms] [-cutoff <real>]
DESCRIPTION
gmx 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 gmx cluster and
then sort the clusters on either lowest energy or average energy.
OPTIONS
Options to specify input files:
-f [<.pdb>] (eiwit.pdb)
Protein data bank file
Options to specify output files:
-od [<.xvg>] (edocked.xvg)
xvgr/xmgr file
-of [<.xvg>] (efree.xvg)
xvgr/xmgr file
-g [<.log>] (anadock.log)
Log file
Other options:
-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none
-[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
Use gmx-anadock online using onworks.net services
