gmx chi [-s [<.gro/.g96/...>]] [-f [<.xtc/.trr/...>]] [-ss [<.dat>]] [-o [<.xvg>]] [-p [<.pdb>]] [-jc [<.xvg>]] [-corr [<.xvg>]] [-g [<.log>]] [-ot [<.xvg>]] [-oh [<.xvg>]] [-rt [<.xvg>]] [-cp [<.xvg>]] [-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>]
gmx 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
(histo-(dihedral)(RESIDUE).xvg) are cumulative over all
residues of each type.
-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
-all, the angles themselves as a function of time for
each residue are printed to separate files
These can be in radians or degrees.
A log file (argument
-g) is also written. This contains
information about the number of residues of each type.
The NMR ^3J coupling constants from the Karplus equation.
a table for each residue of the number of transitions between rotamers per nanosecond, and the order parameter S^2 of each dihedral.
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
The S^2 order parameters are also output to an .xvg file
-o ) and optionally as a .pdb file with
the S^2 values as B-factor (argument
The total number of rotamer transitions per timestep
-ot), the number of transitions per rotamer
-rt), and the ^3J couplings (argument
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.
-chi_prod is set (and
-maxchi > 0), cumulative rotamers, e.g.
(chi_3-1) (if the residue has three 3-fold
-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
is given, the rotamers as functions of time
are written to
and their occupancies to
-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 to specify input files:
-ss[<.dat>] (ssdump.dat) (Optional)
Generic data file
Options to specify output files:
-p[<.pdb>] (order.pdb) (Optional)
Protein data bank file
-corr[<.xvg>] (dihcorr.xvg) (Optional)
-ot[<.xvg>] (dihtrans.xvg) (Optional)
-oh[<.xvg>] (trhisto.xvg) (Optional)
-rt[<.xvg>] (restrans.xvg) (Optional)
-cp[<.xvg>] (chiprodhisto.xvg) (Optional)
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
xvg plot formatting: xmgrace, xmgr, none
Output for phi dihedral angles
Output for psi dihedral angles
Output for omega dihedrals (peptide bonds)
Generate phi/psi and chi_1/chi_2 Ramachandran plots
Write a file that gives 0 or 1 for violated Ramachandran angles
Print dihedral angles modulo 360 degrees
Output separate files for every dihedral.
in angle vs time files, use radians rather than degrees.
Compute chemical shifts from phi/psi angles
bin width for histograms (degrees)
only the central
-core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)
calculate first ndih chi dihedrals: 0, 1, 2, 3, 4, 5, 6
compute average omega as a function of phi/psi and plot it in an .xpm plot
B-factor value for .pdb file for atoms with no calculated dihedral order parameter
compute a single cumulative rotamer for each residue
Include dihedrals to sidechain hydrogens
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.
Length of the ACF, default is half the number of frames
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end
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 gmx rama.
-r0option does not work properly
Rotamers with multiplicity 2 are printed in
chi.logas if they had
multiplicity 3, with the 3rd (g(+)) always having probability 0