Provided by: gromacs-data_4.6.5-1build1_all 
NAME
g_chi - calculates everything you want to know about chi and other dihedrals
VERSION 4.6.5
SYNOPSIS
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
DESCRIPTION
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 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 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.
FILES
-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
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
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)
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-r0 int 1
starting residue
-[no]phino
Output for phi dihedral angles
-[no]psino
Output for psi dihedral angles
-[no]omegano
Output for omega dihedrals (peptide bonds)
-[no]ramano
Generate phi/psi and chi_1/chi_2 Ramachandran plots
-[no]violno
Write a file that gives 0 or 1 for violated Ramachandran angles
-[no]periodicyes
Print dihedral angles modulo 360 degrees
-[no]allno
Output separate files for every dihedral.
-[no]radno
in angle vs time files, use radians rather than degrees.
-[no]shiftno
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
-[no]normhistoyes
Normalize histograms
-[no]ramomegano
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_prodno
compute a single cumulative rotamer for each residue
-[no]HChino
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]normalizeyes
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
KNOWN PROBLEMS
- 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
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 2 Dec 2013 g_chi(1)