1g_chi(1) GROMACS suite, VERSION 4.5 g_chi(1)
2
6 g_chi - calculates everything you want to know about chi and other
7 dihedrals
8 VERSION 4.5
10
12 g_chi -s conf.gro -f traj.xtc -o order.xvg -p order.pdb -ss ssdump.dat
13 -jc Jcoupling.xvg -corr dihcorr.xvg -g chi.log -ot dihtrans.xvg -oh
14 trhisto.xvg -rt restrans.xvg -cp chiprodhisto.xvg -[no]h -[no]version
15 -nice int -b time -e time -dt time -[no]w -xvg enum -r0 int -[no]phi
16 -[no]psi -[no]omega -[no]rama -[no]viol -[no]periodic -[no]all -[no]rad
17 -[no]shift -binwidth int -core_rotamer real -maxchi enum -[no]normhisto
18 -[no]ramomega -bfact real -[no]chi_prod -[no]HChi -bmax real -acflen
19 int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -end‐
20 fit real
21
23 g_chi computes phi, psi, omega and chi dihedrals for all your amino
24 acid backbone and sidechains. It can compute dihedral angle as a func‐
25 tion of time, and as histogram distributions. The distributions
26 (histo-(dihedral)(RESIDUE).xvg) are cumulative over all residues of
27 each type.
28 If option -corr is given, the program will calculate dihedral autocor‐
31 relation functions. The function used is C(t) = cos(chi(tau))
32 cos(chi(tau+t)) . The use of cosines rather than angles themselves,
33 resolves the problem of periodicity. (Van der Spoel & Berendsen
34 (1997), Biophys. J. 72, 2032-2041). Separate files for each dihedral
35 of each residue (corr(dihedral)(RESIDUE)(nresnr).xvg) are output, as
36 well as a file containing the information for all residues (argument of
37 -corr).
38 With option -all, the angles themselves as a function of time for each
41 residue are printed to separate files (dihedral)(RESIDUE)(nresnr).xvg.
42 These can be in radians or degrees.
43 A log file (argument -g) is also written. This contains
46 (a) information about the number of residues of each type.
48 (b) The NMR 3J coupling constants from the Karplus equation.
50 (c) a table for each residue of the number of transitions between
52 rotamers per nanosecond, and the order parameter S2 of each dihedral.
53 (d) a table for each residue of the rotamer occupancy.
55 All rotamers are taken as 3-fold, except for omegas and chi-dihedrals
57 to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu and
58 gln, and chi4 of arg), which are 2-fold. "rotamer 0" means that the
59 dihedral was not in the core region of each rotamer. The width of the
60 core region can be set with -core_rotamer
61 The S2 order parameters are also output to an xvg file (argument -o )
64 and optionally as a pdb file with the S2 values as B-factor (argument
65 -p). The total number of rotamer transitions per timestep (argument
66 -ot), the number of transitions per rotamer (argument -rt), and the 3J
67 couplings (argument -jc), can also be written to .xvg files.
68 If -chi_prod is set (and maxchi 0), cumulative rotamers, e.g.
71 1+9(chi1-1)+3(chi2-1)+(chi3-1) (if the residue has three 3-fold dihe‐
72 drals and maxchi = 3) are calculated. As before, if any dihedral is not
73 in the core region, the rotamer is taken to be 0. The occupancies of
74 these cumulative rotamers (starting with rotamer 0) are written to the
75 file that is the argument of -cp, and if the -all flag is given, the
76 rotamers as functions of time are written to chiprod‐
77 uct(RESIDUE)(nresnr).xvg and their occupancies to histo-chiprod‐
78 uct(RESIDUE)(nresnr).xvg.
79 The option -r generates a contour plot of the average omega angle as a
82 function of the phi and psi angles, that is, in a Ramachandran plot the
83 average omega angle is plotted using color coding.
84
86 -s conf.gro Input
87 Structure file: gro g96 pdb tpr etc.
88 -f traj.xtc Input
90 Trajectory: xtc trr trj gro g96 pdb cpt
91 -o order.xvg Output
93 xvgr/xmgr file
94 -p order.pdb Output, Opt.
96 Protein data bank file
97 -ss ssdump.dat Input, Opt.
99 Generic data file
100 -jc Jcoupling.xvg Output
102 xvgr/xmgr file
103 -corr dihcorr.xvg Output, Opt.
105 xvgr/xmgr file
106 -g chi.log Output
108 Log file
109 -ot dihtrans.xvg Output, Opt.
111 xvgr/xmgr file
112 -oh trhisto.xvg Output, Opt.
114 xvgr/xmgr file
115 -rt restrans.xvg Output, Opt.
117 xvgr/xmgr file
118 -cp chiprodhisto.xvg Output, Opt.
120 xvgr/xmgr file
121
124 -[no]hno
125 Print help info and quit
126 -[no]versionno
128 Print version info and quit
129 -nice int 19
131 Set the nicelevel
132 -b time 0
134 First frame (ps) to read from trajectory
135 -e time 0
137 Last frame (ps) to read from trajectory
138 -dt time 0
140 Only use frame when t MOD dt = first time (ps)
141 -[no]wno
143 View output xvg, xpm, eps and pdb files
144 -xvg enum xmgrace
146 xvg plot formatting: xmgrace, xmgr or none
147 -r0 int 1
149 starting residue
150 -[no]phino
152 Output for Phi dihedral angles
153 -[no]psino
155 Output for Psi dihedral angles
156 -[no]omegano
158 Output for Omega dihedrals (peptide bonds)
159 -[no]ramano
161 Generate Phi/Psi and Chi1/Chi2 ramachandran plots
162 -[no]violno
164 Write a file that gives 0 or 1 for violated Ramachandran angles
165 -[no]periodicyes
167 Print dihedral angles modulo 360 degrees
168 -[no]allno
170 Output separate files for every dihedral.
171 -[no]radno
173 in angle vs time files, use radians rather than degrees.
174 -[no]shiftno
176 Compute chemical shifts from Phi/Psi angles
177 -binwidth int 1
179 bin width for histograms (degrees)
180 -core_rotamer real 0.5
182 only the central -core_rotamer*(360/multiplicity) belongs to each
183 rotamer (the rest is assigned to rotamer 0)
184 -maxchi enum 0
186 calculate first ndih Chi dihedrals: 0, 1, 2, 3, 4, 5 or 6
187 -[no]normhistoyes
189 Normalize histograms
190 -[no]ramomegano
192 compute average omega as a function of phi/psi and plot it in an xpm
193 plot
194 -bfact real -1
196 B-factor value for pdb file for atoms with no calculated dihedral
197 order parameter
198 -[no]chi_prodno
200 compute a single cumulative rotamer for each residue
201 -[no]HChino
203 Include dihedrals to sidechain hydrogens
204 -bmax real 0
206 Maximum B-factor on any of the atoms that make up a dihedral, for the
207 dihedral angle to be considere in the statistics. Applies to database
208 work where a number of X-Ray structures is analyzed. -bmax = 0 means no
209 limit.
210 -acflen int -1
212 Length of the ACF, default is half the number of frames
213 -[no]normalizeyes
215 Normalize ACF
216 -P enum 0
218 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or
219 3
220 -fitfn enum none
222 Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7 or
223 exp9
224 -ncskip int 0
226 Skip N points in the output file of correlation functions
227 -beginfit real 0
229 Time where to begin the exponential fit of the correlation function
230 -endfit real -1
232 Time where to end the exponential fit of the correlation function, -1
233 is until the end
234
237 - Produces MANY output files (up to about 4 times the number of
238 residues in the protein, twice that if autocorrelation functions are
239 calculated). Typically several hundred files are output.
240 - Phi and psi dihedrals are calculated in a non-standard way, using
242 H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead
243 of N-CA-C-N(+). This causes (usually small) discrepancies with the out‐
244 put of other tools like g_rama.
245 - -r0 option does not work properly
247 - Rotamers with multiplicity 2 are printed in chi.log as if they had
249 multiplicity 3, with the 3rd (g(+)) always having probability 0
250
253 gromacs(7)
254 More information about GROMACS is available at <http://www.gro‐
256 macs.org/>.
257 Thu 26 Aug 2010 g_chi(1)