gmx-chi(1) GROMACS Manual gmx-chi(1)NAMEgmx-chi - Calculate everything you want to know about chi and other
dihedrals
SYNOPSIS
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 <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>]
[-beginfit <real>] [-endfit <real>]
DESCRIPTION
gmx chi computes phi, psi, omega, and chi dihedrals for all your amino
acid backbone and sidechains. It can compute dihedral angle as a func‐
tion 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 autocor‐
relation 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 trajec‐
tory 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 occupan‐
cies 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 chiprod‐
uct(RESIDUE)(nresnr).xvg and their occupancies to histo-chiprod‐
uct(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.
OPTIONS
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 phi dihedral angles
-[no]psi (no)
Output for psi dihedral angles
-[no]omega (no)
Output for omega dihedrals (peptide bonds)
-[no]rama (no)
Generate phi/psi and chi_1/chi_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 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, 6
-[no]normhisto (yes)
Normalize histograms
-[no]ramomega (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 (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 data‐
base 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, erf‐
fit
-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
- 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 out‐
put of other tools like gmx 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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-chi(1)
