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GMX-CHI(1) GROMACS GMX-CHI(1) NAME gmx-chi - Calculate everything you want to know about chi and other di- hedrals 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>] [-rN <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, re- solves 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 ro- tamers per nanosecond, and the order parameter S^2 of each dihe- dral. • 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 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 di- hedrals 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 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 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) Time of first frame to read from trajectory (default unit ps) -e <time> (0) Time of last frame to read from trajectory (default unit ps) -dt <time> (0) Only use frame when t MOD dt = first time (default unit 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 -rN <int> (-1) last 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 dihe- dral 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 considered in the statistics. Ap- plies to database work where a number of X-Ray structures is an- alyzed. -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 func- tion -endfit <real> (-1) Time where to end the exponential fit of the correlation func- tion, -1 is until the end KNOWN ISSUES • N-terminal phi and C-terminal 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. • 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 gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-CHI(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | KNOWN ISSUES | SEE ALSO | COPYRIGHT
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