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g_chiMain Table of Contents |
VERSION 3.1
Thu 28 Feb 2002
| VERSION 3.1 |
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. Output is in form of xvgr files, as well as a LaTeX table of the number of transitions per nanosecond.
Order parameters S2 for each of the dihedrals are calculated and output as xvgr file and optionally as a pdb file with the S2 values as B-factor.
If option -c 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).
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.
| option | filename | type | description |
|---|---|---|---|
| -c | conf.gro | Input | Generic structure: gro g96 pdb tpr tpb tpa |
| -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 |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -[no]X | bool | no | Use dialog box GUI to edit command line options |
| -nice | int | 19 | Set the nicelevel |
| -b | time | -1 | First frame (ps) to read from trajectory |
| -e | time | -1 | Last frame (ps) to read from trajectory |
| -dt | time | -1 | Only use frame when t MOD dt = first time (ps) |
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files |
| -r0 | int | 1 | starting residue |
| -[no]phi | bool | no | Output for Phi dihedral angles |
| -[no]psi | bool | no | Output for Psi dihedral angles |
| -[no]omega | bool | no | Output for Omega dihedrals (peptide bonds) |
| -[no]rama | bool | no | Generate Phi/Psi and Chi1/Chi2 ramachandran plots |
| -[no]viol | bool | no | Write a file that gives 0 or 1 for violated Ramachandran angles |
| -[no]all | bool | no | Output separate files for every dihedral. |
| -[no]shift | bool | no | Compute chemical shifts from Phi/Psi angles |
| -run | int | 1 | perform running average over ndeg degrees for histograms |
| -maxchi | enum | 0 | calculate first ndih Chi dihedrals: 0, 1, 2, 3, 4, 5 or 6 |
| -[no]normhisto | bool | yes | Normalize histograms |
| -[no]ramomega | bool | 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 |
| -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 | bool | 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 or exp7 |
| -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 |