g_chi

Main Table of Contents

VERSION 4.6.3
Fri 5 Jul 2013

Description

g_chi computes φ, ψ, ω, and χ 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) = . 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 S^2 of each dihedral.
(d) a table for each residue of the rotamer occupancy.

All rotamers are taken as 3-fold, except for ω and χ dihedrals to planar groups (i.e. χ_2 of aromatics, Asp and Asn; χ_3 of Glu and Gln; and χ_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(χ_1-1)+3(χ_2-1)+(χ_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 ω angle as a function of the φ and ψ angles, that is, in a Ramachandran plot the average ω angle is plotted using color coding.

Files

optionfilenametypedescription
-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

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]version 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 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 bool no Output for φ dihedral angles
-[no]psi bool no Output for ψ dihedral angles
-[no]omega bool no Output for ω dihedrals (peptide bonds)
-[no]rama bool no Generate φ/ψ and χ_1/χ_2 Ramachandran plots
-[no]viol bool no Write a file that gives 0 or 1 for violated Ramachandran angles
-[no]periodic bool yes Print dihedral angles modulo 360 degrees
-[no]all bool no Output separate files for every dihedral.
-[no]rad bool no in angle vs time files, use radians rather than degrees.
-[no]shift bool no Compute chemical shifts from φ/ψ 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 χ dihedrals: 0, 1, 2, 3, 4, 5 or 6
-[no]normhisto bool yes Normalize histograms
-[no]ramomega bool no compute average omega as a function of φ/ψ 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 bool no compute a single cumulative rotamer for each residue
-[no]HChi 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 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, 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

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