Provided by: gromacs-data_2018.1-1_all bug


       gmx-chi - Calculate everything you want to know about chi and other dihedrals


          gmx chi [-s [<.gro/.g96/...>]] [-f [<.xtc/.trr/...>]] [-ss [<.dat>]]
                  [-o [<.xvg>]] [-p [<.pdb>]] [-jc [<.xvg>]] [-corr [<.xvg>]]
                  [-g [<.log>]] [-ot [<.xvg>]] [-oh [<.xvg>]] [-rt [<.xvg>]]
                  [-cp [<.xvg>]] [-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>]
                  [-beginfit <real>] [-endfit <real>]


       gmx  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 degrees.

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

          · information about the number of residues of each type.

          · The NMR ^3J coupling constants from the Karplus equation.

          · a table  for  each  residue  of  the  number  of  transitions  between  rotamers  per
            nanosecond,  and the order parameter S^2 of each dihedral.

          · 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 S^2 order parameters are also output to an .xvg file (argument -o ) and optionally  as
       a  .pdb  file  with the S^2 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.


       Options to specify input files:

       -s [<.gro/.g96/…>] (conf.gro)
              Structure file: gro g96 pdb brk ent esp tpr

       -f [<.xtc/.trr/…>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -ss [<.dat>] (ssdump.dat) (Optional)
              Generic data file

       Options to specify output files:

       -o [<.xvg>] (order.xvg)
              xvgr/xmgr file

       -p [<.pdb>] (order.pdb) (Optional)
              Protein data bank file

       -jc [<.xvg>] (Jcoupling.xvg)
              xvgr/xmgr file

       -corr [<.xvg>] (dihcorr.xvg) (Optional)
              xvgr/xmgr file

       -g [<.log>] (chi.log)
              Log file

       -ot [<.xvg>] (dihtrans.xvg) (Optional)
              xvgr/xmgr file

       -oh [<.xvg>] (trhisto.xvg) (Optional)
              xvgr/xmgr file

       -rt [<.xvg>] (restrans.xvg) (Optional)
              xvgr/xmgr file

       -cp [<.xvg>] (chiprodhisto.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -r0 <int> (1)
              starting residue

       -[no]phi (no)
              Output for phi dihedral angles

       -[no]psi (no)
              Output for psi dihedral angles

       -[no]omega (no)
              Output for omega dihedrals (peptide bonds)

       -[no]rama (no)
              Generate phi/psi and chi_1/chi_2 Ramachandran plots

       -[no]viol (no)
              Write a file that gives 0 or 1 for violated Ramachandran angles

       -[no]periodic (yes)
              Print dihedral angles modulo 360 degrees

       -[no]all (no)
              Output separate files for every dihedral.

       -[no]rad (no)
              in angle vs time files, use radians rather than degrees.

       -[no]shift (no)
              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, 6

       -[no]normhisto (yes)
              Normalize histograms

       -[no]ramomega (no)
              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

       -[no]chi_prod (no)
              compute a single cumulative rotamer for each residue

       -[no]HChi (no)
              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

       -[no]normalize (yes)
              Normalize ACF

       -P <enum> (0)
              Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

       -fitfn <enum> (none)
              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9

       -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


       · 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 gmx 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



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