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GMX-CHI(1)			    GROMACS			    GMX-CHI(1)

NAME
       gmx-chi - Calculate everything you want to know about chi and other di-
       hedrals

SYNOPSIS
	  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_]

DESCRIPTION
       gmx chi computes	phi, psi, omega, and chi dihedrals for all your	 amino
       acid backbone and sidechains.  It can compute dihedral angle as a func-
       tion 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  autocor-
       relation	  functions.  The  function  used  is  C(t)  =	<cos(chi(tau))
       cos(chi(tau+t))>. The use of cosines rather than	angles themselves, re-
       solves  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

	  o information	about the number of residues of	each type.

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

	  o a table for	each residue of	the number of transitions between  ro-
	    tamers  per	nanosecond,  and the order parameter S^2 of each dihe-
	    dral.

	  o 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. arotamer 0a  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 trajec-
       tory 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 di-
       hedrals 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   chiprod-
       uct(RESIDUE)(nresnr).xvg	  and	their  occupancies  to	histo-chiprod-
       uct(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
       Options to specify input	files:

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

       -f [<.xtc/.trr/^a|>] (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	 dihe-
	      dral 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.  Ap-
	      plies to database	work where a number of X-Ray structures	is an-
	      alyzed. -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 func-
	      tion

       -endfit <real> (-1)
	      Time where to end	the exponential	fit of the  correlation	 func-
	      tion, -1 is until	the end

KNOWN ISSUES
       o 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.

       o 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.

       o -r0 option does not work properly

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

SEE ALSO
       gmx(1)

       More	information    about	GROMACS	   is	 available    at    <-
       http://www.gromacs.org/>.

COPYRIGHT
       2020, GROMACS development team

2020.4				 Oct 06, 2020			    GMX-CHI(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | KNOWN ISSUES | SEE ALSO | COPYRIGHT

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