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g_chi_d

NAME

g_chi - calculates everything you want to know about chi and other dihedrals

SYNOPSIS

g_chi -s conf.gro -f traj.xtc -o order.xvg -p order.pdb -ss ssdump.dat -jc Jcoupling.xvg -corr dihcorr.xvg -g chi.log -ot dihtrans.xvg -oh trhisto.xvg -rt restrans.xvg -cp chiprodhisto.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -r0 int -[no]phi -[no]psi -[no]omega -[no]rama -[no]viol -[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 -ncskip int -beginfit real -endfit real

DESCRIPTION

g_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

(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 omegas and chi-dihedrals to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu and gln, and chi4 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.

If -chi_prod is set (and maxchi 0), cumulative rotamers, e.g. 1+9(chi1-1)+3(chi2-1)+(chi3-1) (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.

FILES

-s conf.gro Input
 Generic structure: gro g96 pdb tpr tpb tpa xml 

-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb 

-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

-[no]h no
 Print help 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 no
 View output xvg, xpm, eps and pdb files

-[no]xvgr yes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-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 Chi1/Chi2 ramachandran plots

-[no]viol no
 Write a file that gives 0 or 1 for violated Ramachandran angles

-[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 or 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 or 3

-fitfn enum none
 Fit function:  none , exp , aexp , exp_exp , vac , exp5 , exp7 or exp9

-ncskip int 0
 Skip N 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 till 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 g_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 ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.