gmx-chi - Online in the Cloud

PROGRAM:

NAME

gmx-chi - Calculate everything you want to know about chi and other dihedrals

SYNOPSIS

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>]

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 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

· 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 -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(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 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.

OPTIONS

Options to specify input files:

-s [<.gro/.g96/...>] (conf.gro)
Structure file: gro g96 pdb brk ent esp tpr

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-ss [<.dat>] (ssdump.dat) (Optional)
Generic data file

Options to specify output files:

-o [<.xvg>] (order.xvg)
xvgr/xmgr file

-p [<.pdb>] (order.pdb) (Optional)
Protein data bank file

-jc [<.xvg>] (Jcoupling.xvg)
xvgr/xmgr file

-corr [<.xvg>] (dihcorr.xvg) (Optional)
xvgr/xmgr file

-g [<.log>] (chi.log)
Log file

-ot [<.xvg>] (dihtrans.xvg) (Optional)
xvgr/xmgr file

-oh [<.xvg>] (trhisto.xvg) (Optional)
xvgr/xmgr file

-rt [<.xvg>] (restrans.xvg) (Optional)
xvgr/xmgr file

-cp [<.xvg>] (chiprodhisto.xvg) (Optional)
xvgr/xmgr file

Other options:

-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>
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 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, exp5, exp7, exp9

-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 output 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

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