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g_rmsf
Langue: en
Version: 259853 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_rmsf - calculates atomic fluctuationsSYNOPSIS
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]anisoDESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after first 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 InputGeneric trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-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]h noPrint 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]w no
View output xvg, xpm, eps and pdb files
-[no]xvgr yes
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-[no]res no
Calculate averages for each residue
-[no]aniso no
Compute anisotropic termperature factors
SEE ALSO
gromacs(7)More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre