gmx chi

Main Table of Contents VERSION 5.0.7


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 ] [-b 


gmx 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) = <cos(χ(τ)) cos(χ(τ+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.


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 φ dihedral angles
-[no]psi (no)
Output for ψ dihedral angles
-[no]omega (no)
Output for ω dihedrals (peptide bonds)
-[no]rama (no)
Generate φ/ψ and χ_1/χ_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 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, 6
-[no]normhisto (yes)
Normalize histograms
-[no]ramomega (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 (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 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 (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, erffit
-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