g_chi_d (1) - Linux Manuals
g_chi_d: calculates everything you want to know about chi and other dihedrals
NAMEg_chi - calculates everything you want to know about chi and other dihedrals
SYNOPSISg_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]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 -ncskip int -beginfit real -endfit real
DESCRIPTIONg_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.
FILES-s conf.gro Input
-nice int 19
-b time 0
-e time 0
-dt time 0
-r0 int 1
-binwidth int 1
-core_rotamer real 0.5
-maxchi enum 0
-bfact real -1
-bmax real 0
-acflen int -1
-P enum 0
-fitfn enum none
-ncskip int 0
-beginfit real 0
-endfit real -1
KNOWN PROBLEMS- 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