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g_anadock(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_anadock(1)

NAME
g_anadock - cluster structures from Autodock runs VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_anadock -f eiwit.pdb -ox cluster.pdb -od edocked.xvg -of efree.xvg -g anadock.log -[no]h -[no]version -nice int -xvg enum -[no]free -[no]rms -cutoff real DESCRIPTION
g_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 -[no]versionno Print version info and quit -nice int 0 Set the nicelevel -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[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/>. Mon 4 Apr 2011 g_anadock(1)

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g_disre(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_disre(1)

NAME
g_disre - analyzes distance restraints VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_disre -s topol.tpr -f traj.xtc -ds drsum.xvg -da draver.xvg -dn drnum.xvg -dm drmax.xvg -dr restr.xvg -l disres.log -n viol.ndx -q viol.pdb -c clust.ndx -x matrix.xpm -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -ntop int -maxdr real -nlevels int -[no]third DESCRIPTION
g_disre computes violations of distance restraints. If necessary, all protons can be added to a protein molecule using the g_protonate program. The program always computes the instantaneous violations rather than time-averaged, because this analysis is done from a trajectory file afterwards it does not make sense to use time averaging. However, the time averaged values per restraint are given in the log file. An index file may be used to select specific restraints for printing. When the optional -q flag is given a .pdb file coloured by the amount of average violations. When the -c option is given, an index file will be read containing the frames in your trajectory corresponding to the clusters (defined in another manner) that you want to analyze. For these clusters the program will compute average violations using the third power averaging algorithm and print them in the log file. FILES
-s topol.tpr Input Run input file: tpr tpb tpa -f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -ds drsum.xvg Output xvgr/xmgr file -da draver.xvg Output xvgr/xmgr file -dn drnum.xvg Output xvgr/xmgr file -dm drmax.xvg Output xvgr/xmgr file -dr restr.xvg Output xvgr/xmgr file -l disres.log Output Log file -n viol.ndx Input, Opt. Index file -q viol.pdb Output, Opt. Protein data bank file -c clust.ndx Input, Opt. Index file -x matrix.xpm Output, Opt. X PixMap compatible matrix file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -ntop int 0 Number of large violations that are stored in the log file every step -maxdr real 0 Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data. -nlevels int 20 Number of levels in the matrix output -[no]thirdyes Use inverse third power averaging or linear for matrix output SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_disre(1)
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