1 .TH g_anadock 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_anadock - cluster structures from Autodock runs
5 .B VERSION 4.5.4-dev-20110404-bc5695c
8 .BI "\-f" " eiwit.pdb "
9 .BI "\-ox" " cluster.pdb "
10 .BI "\-od" " edocked.xvg "
11 .BI "\-of" " efree.xvg "
12 .BI "\-g" " anadock.log "
14 .BI "\-[no]version" ""
19 .BI "\-cutoff" " real "
21 \&\fB g_anadock\fR analyses the results of an Autodock run and clusters the
22 \&structures together, based on distance or RMSD. The docked energy
23 \&and free energy estimates are analysed, and for each cluster the
24 \&energy statistics are printed.
27 \&An alternative approach to this is to cluster the structures first
28 \&using \fB g_cluster\fR and then sort the clusters on either lowest
29 \&energy or average energy.
31 .BI "\-f" " eiwit.pdb"
33 Protein data bank file
35 .BI "\-ox" " cluster.pdb"
37 Protein data bank file
39 .BI "\-od" " edocked.xvg"
43 .BI "\-of" " efree.xvg"
47 .BI "\-g" " anadock.log"
53 Print help info and quit
55 .BI "\-[no]version" "no "
56 Print version info and quit
58 .BI "\-nice" " int" " 0"
61 .BI "\-xvg" " enum" " xmgrace"
62 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
64 .BI "\-[no]free" "no "
65 Use Free energy estimate from autodock for sorting the classes
67 .BI "\-[no]rms" "yes "
68 Cluster on RMS or distance
70 .BI "\-cutoff" " real" " 0.2 "
71 Maximum RMSD/distance for belonging to the same cluster
76 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.