Provided by: gromacs-data_4.6.5-1build1_all bug


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

       VERSION 4.6.5


       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  -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum
       -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  -corr).

       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

       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 omega and  chi  dihedrals  to  planar  groups
       (i.e.  chi_2 of aromatics, Asp and Asn; chi_3 of Glu and Gln; and chi_4 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. Note  that
       the  analysis  of  rotamer  transitions  assumes  that  the supplied trajectory frames are
       equally spaced in time.

       If    -chi_prod   is    set    (and     -maxchi     0),    cumulative    rotamers,    e.g.
       1+9(chi_1-1)+3(chi_2-1)+(chi_3-1)  (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  histo-chiproduct(RESIDUE)(nresnr).xvg.

       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 etc.

       -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

        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)

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -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 chi_1/chi_2 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 plot

       -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 limit.

       -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  3

       -fitfn enum none
        Fit function:  none,  exp,  aexp,  exp_exp,  vac,  exp5,  exp7,  exp9 or  erffit

       -ncskip int 0
        Skip this many 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 until 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 <>.

                                          Mon 2 Dec 2013                                 g_chi(1)