Provided by: gromacs-data_4.6.5-1build1_all

**NAME**

g_chi - calculates everything you want to know about chi and other dihedralsVERSION4.6.5

**SYNOPSIS**

g_chi-sconf.gro-ftraj.xtc-oorder.xvg-porder.pdb-ssssdump.dat-jcJcoupling.xvg-corrdihcorr.xvg-gchi.log-otdihtrans.xvg-ohtrhisto.xvg-rtrestrans.xvg-cpchiprodhisto.xvg-[no]h-[no]version-niceint-btime-etime-dttime-[no]w-xvgenum-r0int-[no]phi-[no]psi-[no]omega-[no]rama-[no]viol-[no]periodic-[no]all-[no]rad-[no]shift-binwidthint-core_rotamerreal-maxchienum-[no]normhisto-[no]ramomega-bfactreal-[no]chi_prod-[no]HChi-bmaxreal-acflenint-[no]normalize-Penum-fitfnenum-ncskipint-beginfitreal-endfitreal

**DESCRIPTION**

g_chicomputes 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-corris 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 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_rotamerThe S2 order parameters are also output to an.xvgfile (argument-o) and optionally as a.pdbfile 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.xvgfiles. Note that the analysis of rotamer transitions assumes that the supplied trajectory frames are equally spaced in time. If-chi_prodis set (and-maxchi0), 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-allflag is given, the rotamers as functions of time are written tochiproduct(RESIDUE)(nresnr).xvgand their occupancies tohisto-chiproduct(RESIDUE)(nresnr).xvg. The option-rgenerates 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**

-sconf.groInputStructure file: gro g96 pdb tpr etc.-ftraj.xtcInputTrajectory: xtc trr trj gro g96 pdb cpt-oorder.xvgOutputxvgr/xmgr file-porder.pdbOutput,Opt.Protein data bank file-ssssdump.datInput,Opt.Generic data file-jcJcoupling.xvgOutputxvgr/xmgr file-corrdihcorr.xvgOutput,Opt.xvgr/xmgr file-gchi.logOutputLog file-otdihtrans.xvgOutput,Opt.xvgr/xmgr file-ohtrhisto.xvgOutput,Opt.xvgr/xmgr file-rtrestrans.xvgOutput,Opt.xvgr/xmgr file-cpchiprodhisto.xvgOutput,Opt.xvgr/xmgr file

**OTHER** **OPTIONS**

-[no]hnoPrint help info and quit-[no]versionnoPrint version info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-dttime0Only use frame when t MOD dt = first time (ps)-[no]wnoView output.xvg,.xpm,.epsand.pdbfiles-xvgenumxmgracexvg plot formatting:xmgrace,xmgrornone-r0int1starting residue-[no]phinoOutput for phi dihedral angles-[no]psinoOutput for psi dihedral angles-[no]omeganoOutput for omega dihedrals (peptide bonds)-[no]ramanoGenerate phi/psi and chi_1/chi_2 Ramachandran plots-[no]violnoWrite a file that gives 0 or 1 for violated Ramachandran angles-[no]periodicyesPrint dihedral angles modulo 360 degrees-[no]allnoOutput separate files for every dihedral.-[no]radnoin angle vs time files, use radians rather than degrees.-[no]shiftnoCompute chemical shifts from phi/psi angles-binwidthint1bin width for histograms (degrees)-core_rotamerreal0.5only the central-core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)-maxchienum0calculate first ndih chi dihedrals:0,1,2,3,4,5or6-[no]normhistoyesNormalize histograms-[no]ramomeganocompute average omega as a function of phi/psi and plot it in an.xpmplot-bfactreal-1B-factor value for.pdbfile for atoms with no calculated dihedral order parameter-[no]chi_prodnocompute a single cumulative rotamer for each residue-[no]HChinoInclude dihedrals to sidechain hydrogens-bmaxreal0Maximum 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.-acflenint-1Length of the ACF, default is half the number of frames-[no]normalizeyesNormalize ACF-Penum0Order of Legendre polynomial for ACF (0 indicates none):0,1,2or3-fitfnenumnoneFit function:none,exp,aexp,exp_exp,vac,exp5,exp7,exp9orerffit-ncskipint0Skip this many points in the output file of correlation functions-beginfitreal0Time where to begin the exponential fit of the correlation function-endfitreal-1Time where to end the exponential fit of the correlation function, -1 is until the end

**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 likeg_rama. --r0option does not work properly - Rotamers with multiplicity 2 are printed inchi.logas if they had multiplicity 3, with the 3rd (g(+)) always having probability 0

**SEE** **ALSO**

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_chi(1)