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)