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gmx-chi(1)			GROMACS	Manual			    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/...>]] [-o [<.xvg>]]
	       [-p [<.pdb>]] [-ss [<.dat>]] [-jc [<.xvg>]] [-corr [<.xvg>]]
	       [-g [<.log>]] [-ot [<.xvg>]] [-oh [<.xvg>]] [-rt	[<.xvg>]]
	       [-cp [<.xvg>]] [-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>]
	       [-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 (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 or-
       der 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  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	and output files:

       -s [_.gro/.g96/..._] (conf.gro) (Input)
	   Structure file: gro g96 pdb brk ent esp tpr tpb tpa

       -f [_.xtc/.trr/..._] (traj.xtc) (Input)
	   Trajectory: xtc trr cpt trj gro g96 pdb tng

       -o [_.xvg_] (order.xvg) (Output)
	   xvgr/xmgr file

       -p [_.pdb_] (order.pdb) (Output,	Optional)
	   Protein data	bank file

       -ss [_.dat_] (ssdump.dat) (Input, Optional)
	   Generic data	file

       -jc [_.xvg_] (Jcoupling.xvg) (Output)
	   xvgr/xmgr file

       -corr [_.xvg_] (dihcorr.xvg) (Output, Optional)
	   xvgr/xmgr file

       -g [_.log_] (chi.log) (Output)
	   Log file

       -ot [_.xvg_] (dihtrans.xvg) (Output, Optional)
	   xvgr/xmgr file

       -oh [_.xvg_] (trhisto.xvg) (Output, Optional)
	   xvgr/xmgr file

       -rt [_.xvg_] (restrans.xvg) (Output, Optional)
	   xvgr/xmgr file

       -cp [_.xvg_] (chiprodhisto.xvg) (Output,	Optional)
	   xvgr/xmgr file

       Other options:

       -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]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 data-
       base 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, vac,	exp5, exp7, exp9, erf-
       fit

       -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

KNOWN ISSUES
       -  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 out-
       put 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

SEE ALSO
       gromacs(7)

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

VERSION	5.0.6							    gmx-chi(1)

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

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