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_rmsf(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_rmsf(1)NAME
g_rmsf - calculates atomic fluctuations
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_rmsf -f traj.xtc -s topol.tpr -n index.ndx -q eiwit.pdb -oq bfac.pdb -ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg -dir
rmsf.log -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]res -[no]aniso -[no]fit
DESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory (supplied with -f)
after (optionally) fitting to a reference frame (supplied with -s).
With option -oq the RMSF values are converted to B-factor values, which are written to a .pdb file with the coordinates, of the structure
file, or of a .pdb file when -q is specified. Option -ox writes the B-factors to a file with the average coordinates.
With the option -od the root mean square deviation with respect to the reference structure is calculated.
With the option -aniso, g_rmsf will compute anisotropic temperature factors and then it will also output average coordinates and a .pdb
file with ANISOU records (corresonding to the -oq or -ox option). Please note that the U values are orientation-dependent, so before com-
parison with experimental data you should verify that you fit to the experimental coordinates.
When a .pdb input file is passed to the program and the -aniso flag is set a correlation plot of the Uij will be created, if any aniso-
tropic temperature factors are present in the .pdb file.
With option -dir the average MSF (3x3) matrix is diagonalized. This shows the directions in which the atoms fluctuate the most and the
least.
FILES -f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-q eiwit.pdb Input, Opt.
Protein data bank file
-oq bfac.pdb Output, Opt.
Protein data bank file
-ox xaver.pdb Output, Opt.
Protein data bank file
-o rmsf.xvg Output
xvgr/xmgr file
-od rmsdev.xvg Output, Opt.
xvgr/xmgr file
-oc correl.xvg Output, Opt.
xvgr/xmgr file
-dir rmsf.log Output, Opt.
Log 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
-[no]resno
Calculate averages for each residue
-[no]anisono
Compute anisotropic termperature factors
-[no]fityes
Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory
match.
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_rmsf(1)