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       g_chi  -  calculates  everything  you  want to know about chi and other

       VERSION 4.0.1


       g_chi -s conf.gro -f traj.xtc -o order.xvg -p order.pdb -ss  ssdump.dat
       -jc  Jcoupling.xvg  -corr  dihcorr.xvg  -g chi.log -ot dihtrans.xvg -oh
       trhisto.xvg -rt restrans.xvg -cp chiprodhisto.xvg -[no]h -nice  int  -b
       time  -e  time  -dt  time  -[no]w  -[no]xvgr  -r0 int -[no]phi -[no]psi
       -[no]omega  -[no]rama   -[no]viol   -[no]periodic   -[no]all   -[no]rad
       -[no]shift -binwidth int -core_rotamer real -maxchi enum -[no]normhisto
       -[no]ramomega -bfact real -[no]chi_prod -[no]HChi  -bmax  real  -acflen
       int  -[no]normalize  -P  enum  -fitfn  enum  -ncskip int -beginfit real
       -endfit real


       g_chi computes phi, psi, omega and chi dihedrals  for  all  your  amino
       acid  backbone  and  sidechains.   It  can  compute dihedral angle as a
       function of time, and as histogram  distributions.   The  distributions
       (histo-(dihedral)(RESIDUE).xvg)  are  cumulative  over  all residues of
       each type.

       If  option   -corr  is  given,  the  program  will  calculate  dihedral
       autocorrelation  functions.  The function used is C(t) =  cos(chi(tau))
       cos(chi(tau+t)) . The use of cosines  rather  than  angles  themselves,
       resolves  the  problem  of  periodicity.   (Van  der  Spoel & Berendsen
       (1997),  Biophys. J. 72, 2032-2041).  Separate files for each  dihedral
       of  each  residue  (corr(dihedral)(RESIDUE)(nresnr).xvg) are output, as
       well as a file containing the information for all residues (argument of

       With option  -all, the angles themselves as a function of time for each
       residue are printed to separate files  (dihedral)(RESIDUE)(nresnr).xvg.
       These can be in radians or degrees.

       A log file (argument  -g) is also written. This contains

       (a) information about the number of residues of each type.

       (b) The NMR 3J coupling constants from the Karplus equation.

       (c)  a  table  for  each  residue  of the number of transitions between
       rotamers per nanosecond,  and the order parameter S2 of each  dihedral.

       (d) a table for each residue of the rotamer occupancy.

       All  rotamers  are taken as 3-fold, except for omegas and chi-dihedrals
       to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of  glu  and
       gln,  and  chi4  of  arg), which are 2-fold. "rotamer 0" means that the
       dihedral was not in the core region of each rotamer.  The width of  the
       core region can be set with  -core_rotamer

       The  S2 order parameters are also output to an xvg file (argument  -o )
       and optionally as a pdb file with the S2 values as  B-factor  (argument
       -p).   The  total  number of rotamer transitions per timestep (argument
       -ot), the number of transitions per rotamer (argument  -rt), and the 3J
       couplings (argument  -jc), can also be written to .xvg files.

       If   -chi_prod  is  set  (and  maxchi   0),  cumulative  rotamers, e.g.
       1+9(chi1-1)+3(chi2-1)+(chi3-1)  (if  the  residue  has   three   3-fold
       dihedrals and maxchi = 3) are calculated. As before, if any dihedral is
       not in the core region, the rotamer is taken to be 0.  The  occupancies
       of  these  cumulative rotamers (starting with rotamer 0) are written to
       the file that is the argument of  -cp, and if the  -all flag is  given,
       the    rotamers    as    functions    of    time    are    written   to
       chiproduct(RESIDUE)(nresnr).xvg    and     their     occupancies     to

       The option  -r generates a contour plot of the average omega angle as a
       function of the phi and psi angles, that is, in a Ramachandran plot the
       average omega angle is plotted using color coding.


       -s conf.gro Input
        Structure file: gro g96 pdb tpr tpb tpa

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -o order.xvg Output
        xvgr/xmgr file

       -p order.pdb Output, Opt.
        Protein data bank file

       -ss ssdump.dat Input, Opt.
        Generic data file

       -jc Jcoupling.xvg Output
        xvgr/xmgr file

       -corr dihcorr.xvg Output, Opt.
        xvgr/xmgr file

       -g chi.log Output
        Log file

       -ot dihtrans.xvg Output, Opt.
        xvgr/xmgr file

       -oh trhisto.xvg Output, Opt.
        xvgr/xmgr file

       -rt restrans.xvg Output, Opt.
        xvgr/xmgr file

       -cp chiprodhisto.xvg Output, Opt.
        xvgr/xmgr file


        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)

        View output xvg, xpm, eps and pdb files

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -r0 int 1
        starting residue

        Output for Phi dihedral angles

        Output for Psi dihedral angles

        Output for Omega dihedrals (peptide bonds)

        Generate Phi/Psi and Chi1/Chi2 ramachandran plots

        Write a file that gives 0 or 1 for violated Ramachandran angles

        Print dihedral angles modulo 360 degrees

        Output separate files for every dihedral.

        in angle vs time files, use radians rather than degrees.

        Compute chemical shifts from Phi/Psi angles

       -binwidth int 1
        bin width for histograms (degrees)

       -core_rotamer real 0.5
        only the  central  -core_rotamer*(360/multiplicity)  belongs  to  each
       rotamer (the rest is assigned to rotamer 0)

       -maxchi enum 0
        calculate first ndih Chi dihedrals:  0,  1,  2,  3,  4,  5 or  6

        Normalize histograms

        compute  average  omega as a function of phi/psi and plot it in an xpm

       -bfact real -1
        B-factor value for pdb file for  atoms  with  no  calculated  dihedral
       order parameter

        compute a single cumulative rotamer for each residue

        Include dihedrals to sidechain hydrogens

       -bmax real 0
        Maximum  B-factor on any of the atoms that make up a dihedral, for the
       dihedral angle to be considere in the statistics. Applies  to  database
       work where a number of X-Ray structures is analyzed. -bmax = 0 means no

       -acflen int -1
        Length of the ACF, default is half the number of frames

        Normalize ACF

       -P enum 0
        Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or

       -fitfn enum none
        Fit  function:   none,   exp,   aexp,   exp_exp,  vac,  exp5,  exp7 or

       -ncskip int 0
        Skip N points in the output file of correlation functions

       -beginfit real 0
        Time where to begin the exponential fit of the correlation function

       -endfit real -1
        Time where to end the exponential fit of the correlation function,  -1
       is till the end


       -  Produces  MANY  output  files  (up  to  about  4 times the number of
       residues in the protein, twice that if  autocorrelation  functions  are
       calculated). Typically several hundred files are output.

       -  Phi  and  psi  dihedrals are calculated in a non-standard way, using
       H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for  psi  instead
       of  N-CA-C-N(+).  This  causes  (usually  small) discrepancies with the
       output of other tools like g_rama.

       - -r0 option does not work properly

       - Rotamers with multiplicity 2 are printed in chi.log as  if  they  had
       multiplicity 3, with the 3rd (g(+)) always having probability 0



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                       g_chi(1)