Rechercher une page de manuel
g_rmsf
Langue: en
Version: 148633 (fedora - 04/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_rmsf - calculates atomic fluctuationsVERSION 4.0.1
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 -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]res -[no]aniso -[no]fitDESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame.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 comparison 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 anisotropic 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 InputTrajectory: 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]hnoPrint help 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
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-[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/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre