1GMX-ANADOCK(1)                      GROMACS                     GMX-ANADOCK(1)
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NAME

6       gmx-anadock - Cluster structures from Autodock runs
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SYNOPSIS

9          gmx anadock [-f [<.pdb>]] [-od [<.xvg>]] [-of [<.xvg>]] [-g [<.log>]]
10                      [-xvg <enum>] [-[no]free] [-[no]rms] [-cutoff <real>]
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DESCRIPTION

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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OPTIONS

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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SEE ALSO

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       2020, GROMACS development team
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652019.6                           Feb 28, 2020                   GMX-ANADOCK(1)
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