g_disre (1) - Linux Manuals

g_disre: analyzes distance restraints

NAME

g_disre - analyzes distance restraints

VERSION 4.0.1

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 -nice int -b time -e time -dt time -[no]w -[no]xvgr -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 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

-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

-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