AutoDock version 4.2.3 is installed on all nodes (x86-64)  under /usr/local/bin, MGLTools is installed on ark10  under /usr/local/MGLTools-1.5.4.  In order to start adt you'll need X11 forwarding enabled (i.e. start ssh with -X option).

On ark10 there is also submit4.py script located in /usr/local/bin that can be used to submit AutoDock jobs as described in Using AutoDock 4 for Virtual Screening tutorial. Here is a script from this tutorial that shows usage example:

foreach d (`cat ../etc/docking.list`)
    echo $d
    cd $d
    echo "autodock4 -p $d.dpf -l $d.dlg"
    submit4.py $d 1
    cp ../../../Results4/dlgs/"$d".dlg .
    cd ..
    end

There following commands can be used to check job status or to delete batch jobs:

• qstat - show status of batch jobs
• qdel - delete batch jobs