1GMX-ANADOCK(1) GROMACS GMX-ANADOCK(1)
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6 gmx-anadock - Cluster structures from Autodock runs
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9 gmx anadock [-f [<.pdb>]] [-od [<.xvg>]] [-of [<.xvg>]] [-g [<.log>]]
10 [-xvg <enum>] [-[no]free] [-[no]rms] [-cutoff <real>]
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13 gmx anadock analyses the results of an Autodock run and clusters the
14 structures together, based on distance or RMSD. The docked energy and
15 free energy estimates are analysed, and for each cluster the energy
16 statistics are printed.
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18 An alternative approach to this is to cluster the structures first
19 using gmx cluster and then sort the clusters on either lowest energy or
20 average energy.
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23 Options to specify input files:
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25 -f [<.pdb>] (eiwit.pdb)
26 Protein data bank file
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28 Options to specify output files:
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30 -od [<.xvg>] (edocked.xvg)
31 xvgr/xmgr file
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33 -of [<.xvg>] (efree.xvg)
34 xvgr/xmgr file
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36 -g [<.log>] (anadock.log)
37 Log file
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39 Other options:
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41 -xvg <enum> (xmgrace)
42 xvg plot formatting: xmgrace, xmgr, none
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44 -[no]free (no)
45 Use Free energy estimate from autodock for sorting the classes
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47 -[no]rms (yes)
48 Cluster on RMS or distance
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50 -cutoff <real> (0.2)
51 Maximum RMSD/distance for belonging to the same cluster
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54 gmx(1)
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56 More information about GROMACS is available at <‐
57 http://www.gromacs.org/>.
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60 2019, GROMACS development team
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652019.4 Oct 02, 2019 GMX-ANADOCK(1)