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NAME

       anadock - cluster structures from Autodock runs

       VERSION 4.0.1

SYNOPSIS

       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

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

       -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

       -[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

SEE ALSO

       gromacs(7)

       More     information     about     GROMACS     is     available      at
       <http://www.gromacs.org/>.

                                Thu 16 Oct 2008                     anadock(1)