1g_anadock(1)              GROMACS suite, VERSION 4.5              g_anadock(1)
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NAME

6       g_anadock - cluster structures from Autodock runs
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8       VERSION 4.5
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SYNOPSIS

11       g_anadock -f eiwit.pdb -ox cluster.pdb -od edocked.xvg -of efree.xvg -g
12       anadock.log -[no]h -[no]version -nice int -xvg enum -[no]free  -[no]rms
13       -cutoff real
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DESCRIPTION

16       anadock analyses the results of an Autodock run and clusters the struc‐
17       tures together, based on distance or RMSD. The docked energy  and  free
18       energy  estimates are analysed, and for each cluster the energy statis‐
19       tics are printed.
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22       An alternative approach to this is  to  cluster  the  structures  first
23       (using  g_cluster and then sort the clusters on either lowest energy or
24       average energy.
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FILES

27       -f eiwit.pdb Input
28        Protein data bank file
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30       -ox cluster.pdb Output
31        Protein data bank file
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33       -od edocked.xvg Output
34        xvgr/xmgr file
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36       -of efree.xvg Output
37        xvgr/xmgr file
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39       -g anadock.log Output
40        Log file
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OTHER OPTIONS

44       -[no]hno
45        Print help info and quit
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47       -[no]versionno
48        Print version info and quit
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50       -nice int 0
51        Set the nicelevel
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53       -xvg enum xmgrace
54        xvg plot formatting:  xmgrace,  xmgr or  none
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56       -[no]freeno
57        Use Free energy estimate from autodock for sorting the classes
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59       -[no]rmsyes
60        Cluster on RMS or distance
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62       -cutoff real 0.2
63        Maximum RMSD/distance for belonging to the same cluster
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SEE ALSO

67       gromacs(7)
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69       More  information  about  GROMACS  is  available  at   <http://www.gro‐
70       macs.org/>.
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74                                Thu 26 Aug 2010                   g_anadock(1)
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