1 .TH g_chi 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
3 g_chi - calculates everything you want to know about chi and other dihedrals
10 .BI "\-o" " order.xvg "
11 .BI "\-p" " order.pdb "
12 .BI "\-ss" " ssdump.dat "
13 .BI "\-jc" " Jcoupling.xvg "
14 .BI "\-corr" " dihcorr.xvg "
16 .BI "\-ot" " dihtrans.xvg "
17 .BI "\-oh" " trhisto.xvg "
18 .BI "\-rt" " restrans.xvg "
19 .BI "\-cp" " chiprodhisto.xvg "
21 .BI "\-[no]version" ""
34 .BI "\-[no]periodic" ""
38 .BI "\-binwidth" " int "
39 .BI "\-core_rotamer" " real "
40 .BI "\-maxchi" " enum "
41 .BI "\-[no]normhisto" ""
42 .BI "\-[no]ramomega" ""
43 .BI "\-bfact" " real "
44 .BI "\-[no]chi_prod" ""
47 .BI "\-acflen" " int "
48 .BI "\-[no]normalize" ""
50 .BI "\-fitfn" " enum "
51 .BI "\-ncskip" " int "
52 .BI "\-beginfit" " real "
53 .BI "\-endfit" " real "
55 \&\fB g_chi\fR computes phi, psi, omega, and chi dihedrals for all your
56 \&amino acid backbone and sidechains.
57 \&It can compute dihedral angle as a function of time, and as
58 \&histogram distributions.
59 \&The distributions \fB (histo\-(dihedral)(RESIDUE).xvg\fR) are cumulative over all residues of each type.
62 \&If option \fB \-corr\fR is given, the program will
63 \&calculate dihedral autocorrelation functions. The function used
64 \&is C(t) = cos(chi(tau)) cos(chi(tau+t)). The use of cosines
65 \&rather than angles themselves, resolves the problem of periodicity.
66 \&(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032\-2041).
67 \&Separate files for each dihedral of each residue
68 \&\fB (corr(dihedral)(RESIDUE)(nresnr).xvg\fR) are output, as well as a
69 \&file containing the information for all residues (argument of \fB \-corr\fR).
72 \&With option \fB \-all\fR, the angles themselves as a function of time for
73 \&each residue are printed to separate files \fB (dihedral)(RESIDUE)(nresnr).xvg\fR.
74 \&These can be in radians or degrees.
77 \&A log file (argument \fB \-g\fR) is also written. This contains
79 \&(a) information about the number of residues of each type.
81 \&(b) The NMR 3J coupling constants from the Karplus equation.
83 \&(c) a table for each residue of the number of transitions between
84 \&rotamers per nanosecond, and the order parameter S2 of each dihedral.
86 \&(d) a table for each residue of the rotamer occupancy.
89 \&All rotamers are taken as 3\-fold, except for omega and chi dihedrals
90 \&to planar groups (i.e. chi_2 of aromatics, Asp and Asn; chi_3 of Glu
91 \&and Gln; and chi_4 of Arg), which are 2\-fold. "rotamer 0" means
92 \&that the dihedral was not in the core region of each rotamer.
93 \&The width of the core region can be set with \fB \-core_rotamer\fR
96 \&The S2 order parameters are also output to an \fB .xvg\fR file
97 \&(argument \fB \-o\fR ) and optionally as a \fB .pdb\fR file with
98 \&the S2 values as B\-factor (argument \fB \-p\fR).
99 \&The total number of rotamer transitions per timestep
100 \&(argument \fB \-ot\fR), the number of transitions per rotamer
101 \&(argument \fB \-rt\fR), and the 3J couplings (argument \fB \-jc\fR),
102 \&can also be written to \fB .xvg\fR files. Note that the analysis
103 \&of rotamer transitions assumes that the supplied trajectory frames
104 \&are equally spaced in time.
107 \&If \fB \-chi_prod\fR is set (and \fB \-maxchi\fR 0), cumulative rotamers, e.g.
108 \&1+9(chi_1\-1)+3(chi_2\-1)+(chi_3\-1) (if the residue has three 3\-fold
109 \&dihedrals and \fB \-maxchi\fR = 3)
110 \&are calculated. As before, if any dihedral is not in the core region,
111 \&the rotamer is taken to be 0. The occupancies of these cumulative
112 \&rotamers (starting with rotamer 0) are written to the file
113 \&that is the argument of \fB \-cp\fR, and if the \fB \-all\fR flag
114 \&is given, the rotamers as functions of time
115 \&are written to \fB chiproduct(RESIDUE)(nresnr).xvg\fR
116 \&and their occupancies to \fB histo\-chiproduct(RESIDUE)(nresnr).xvg\fR.
119 \&The option \fB \-r\fR generates a contour plot of the average omega angle
120 \&as a function of the phi and psi angles, that is, in a Ramachandran plot
121 \&the average omega angle is plotted using color coding.
123 .BI "\-s" " conf.gro"
125 Structure file: gro g96 pdb tpr etc.
127 .BI "\-f" " traj.xtc"
129 Trajectory: xtc trr trj gro g96 pdb cpt
131 .BI "\-o" " order.xvg"
135 .BI "\-p" " order.pdb"
137 Protein data bank file
139 .BI "\-ss" " ssdump.dat"
143 .BI "\-jc" " Jcoupling.xvg"
147 .BI "\-corr" " dihcorr.xvg"
155 .BI "\-ot" " dihtrans.xvg"
159 .BI "\-oh" " trhisto.xvg"
163 .BI "\-rt" " restrans.xvg"
167 .BI "\-cp" " chiprodhisto.xvg"
173 Print help info and quit
175 .BI "\-[no]version" "no "
176 Print version info and quit
178 .BI "\-nice" " int" " 19"
181 .BI "\-b" " time" " 0 "
182 First frame (ps) to read from trajectory
184 .BI "\-e" " time" " 0 "
185 Last frame (ps) to read from trajectory
187 .BI "\-dt" " time" " 0 "
188 Only use frame when t MOD dt = first time (ps)
191 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
193 .BI "\-xvg" " enum" " xmgrace"
194 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
196 .BI "\-r0" " int" " 1"
199 .BI "\-[no]phi" "no "
200 Output for phi dihedral angles
202 .BI "\-[no]psi" "no "
203 Output for psi dihedral angles
205 .BI "\-[no]omega" "no "
206 Output for omega dihedrals (peptide bonds)
208 .BI "\-[no]rama" "no "
209 Generate phi/psi and chi_1/chi_2 Ramachandran plots
211 .BI "\-[no]viol" "no "
212 Write a file that gives 0 or 1 for violated Ramachandran angles
214 .BI "\-[no]periodic" "yes "
215 Print dihedral angles modulo 360 degrees
217 .BI "\-[no]all" "no "
218 Output separate files for every dihedral.
220 .BI "\-[no]rad" "no "
221 in angle vs time files, use radians rather than degrees.
223 .BI "\-[no]shift" "no "
224 Compute chemical shifts from phi/psi angles
226 .BI "\-binwidth" " int" " 1"
227 bin width for histograms (degrees)
229 .BI "\-core_rotamer" " real" " 0.5 "
230 only the central \fB \-core_rotamer\fR*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)
232 .BI "\-maxchi" " enum" " 0"
233 calculate first ndih chi dihedrals: \fB 0\fR, \fB 1\fR, \fB 2\fR, \fB 3\fR, \fB 4\fR, \fB 5\fR or \fB 6\fR
235 .BI "\-[no]normhisto" "yes "
238 .BI "\-[no]ramomega" "no "
239 compute average omega as a function of phi/psi and plot it in an \fB .xpm\fR plot
241 .BI "\-bfact" " real" " \-1 "
242 B\-factor value for \fB .pdb\fR file for atoms with no calculated dihedral order parameter
244 .BI "\-[no]chi_prod" "no "
245 compute a single cumulative rotamer for each residue
247 .BI "\-[no]HChi" "no "
248 Include dihedrals to sidechain hydrogens
250 .BI "\-bmax" " real" " 0 "
251 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. \fB \-bmax\fR = 0 means no limit.
253 .BI "\-acflen" " int" " \-1"
254 Length of the ACF, default is half the number of frames
256 .BI "\-[no]normalize" "yes "
259 .BI "\-P" " enum" " 0"
260 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR
262 .BI "\-fitfn" " enum" " none"
263 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
265 .BI "\-ncskip" " int" " 0"
266 Skip this many points in the output file of correlation functions
268 .BI "\-beginfit" " real" " 0 "
269 Time where to begin the exponential fit of the correlation function
271 .BI "\-endfit" " real" " \-1 "
272 Time where to end the exponential fit of the correlation function, \-1 is until the end
275 \- 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.
277 \- 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 \fB g_rama\fR.
279 \- \fB \-r0\fR option does not work properly
281 \- Rotamers with multiplicity 2 are printed in \fB chi.log\fR as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0
286 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.