Main Table of Contents

Thu 26 Aug 2010


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 omegas and chi-dihedrals to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu and gln, and chi4 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.

If -chi_prod is set (and maxchi > 0), cumulative rotamers, e.g. 1+9(chi1-1)+3(chi2-1)+(chi3-1) (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

Other options

-[no]h gmx_bool no Print help info and quit
-[no]version gmx_bool no 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]w gmx_bool no View output xvg, xpm, eps and pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-r0 int 1 starting residue
-[no]phi gmx_bool no Output for Phi dihedral angles
-[no]psi gmx_bool no Output for Psi dihedral angles
-[no]omega gmx_bool no Output for Omega dihedrals (peptide bonds)
-[no]rama gmx_bool no Generate Phi/Psi and Chi1/Chi2 ramachandran plots
-[no]viol gmx_bool no Write a file that gives 0 or 1 for violated Ramachandran angles
-[no]periodic gmx_bool yes Print dihedral angles modulo 360 degrees
-[no]all gmx_bool no Output separate files for every dihedral.
-[no]rad gmx_bool no in angle vs time files, use radians rather than degrees.
-[no]shift gmx_bool 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 or 6
-[no]normhisto gmx_bool yes Normalize histograms
-[no]ramomega gmx_bool 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 gmx_bool no compute a single cumulative rotamer for each residue
-[no]HChi gmx_bool 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 gmx_bool yes 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 or exp9
-ncskip int 0 Skip N 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