1GMX-CHI(1) GROMACS GMX-CHI(1)
2
6 gmx-chi - Calculate everything you want to know about chi and other di‐
7 hedrals
8
10 gmx chi [-s [<.gro/.g96/...>]] [-f [<.xtc/.trr/...>]] [-ss [<.dat>]]
11 [-o [<.xvg>]] [-p [<.pdb>]] [-jc [<.xvg>]] [-corr [<.xvg>]]
12 [-g [<.log>]] [-ot [<.xvg>]] [-oh [<.xvg>]] [-rt [<.xvg>]]
13 [-cp [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
14 [-xvg <enum>] [-r0 <int>] [-[no]phi] [-[no]psi] [-[no]omega]
15 [-[no]rama] [-[no]viol] [-[no]periodic] [-[no]all] [-[no]rad]
16 [-[no]shift] [-binwidth <int>] [-core_rotamer <real>]
17 [-maxchi <enum>] [-[no]normhisto] [-[no]ramomega]
18 [-bfact <real>] [-[no]chi_prod] [-[no]HChi] [-bmax <real>]
19 [-acflen <int>] [-[no]normalize] [-P <enum>] [-fitfn <enum>]
20 [-beginfit <real>] [-endfit <real>]
21
23 gmx 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‐
30 relation functions. The function used is C(t) = <cos(chi(tau))
31 cos(chi(tau+t))>. The use of cosines rather than angles themselves, re‐
32 solves the problem of periodicity. (Van der Spoel & Berendsen (1997),
33 Biophys. J. 72, 2032-2041). Separate files for each dihedral of each
34 residue (corr(dihedral)(RESIDUE)(nresnr).xvg) are output, as well as a
35 file containing the information for all residues (argument of -corr).
36 With option -all, the angles themselves as a function of time for each
38 residue are printed to separate files (dihedral)(RESIDUE)(nresnr).xvg.
39 These can be in radians or degrees.
40 A log file (argument -g) is also written. This contains
42 • information about the number of residues of each type.
44 • The NMR ^3J coupling constants from the Karplus equation.
46 • a table for each residue of the number of transitions between ro‐
48 tamers per nanosecond, and the order parameter S^2 of each dihe‐
49 dral.
50 • a table for each residue of the rotamer occupancy.
52 All rotamers are taken as 3-fold, except for omega and chi dihedrals to
54 planar groups (i.e. chi_2 of aromatics, Asp and Asn; chi_3 of Glu and
55 Gln; and chi_4 of Arg), which are 2-fold. "rotamer 0" means that the
56 dihedral was not in the core region of each rotamer. The width of the
57 core region can be set with -core_rotamer
58 The S^2 order parameters are also output to an .xvg file (argument -o )
60 and optionally as a .pdb file with the S^2 values as B-factor (argument
61 -p). The total number of rotamer transitions per timestep (argument
62 -ot), the number of transitions per rotamer (argument -rt), and the ^3J
63 couplings (argument -jc), can also be written to .xvg files. Note that
64 the analysis of rotamer transitions assumes that the supplied trajec‐
65 tory frames are equally spaced in time.
66 If -chi_prod is set (and -maxchi > 0), cumulative rotamers, e.g.
68 1+9(chi_1-1)+3(chi_2-1)+ (chi_3-1) (if the residue has three 3-fold di‐
69 hedrals and -maxchi >= 3) are calculated. As before, if any dihedral is
70 not in the core region, the rotamer is taken to be 0. The occupancies
71 of these cumulative rotamers (starting with rotamer 0) are written to
72 the file that is the argument of -cp, and if the -all flag is given,
73 the rotamers as functions of time are written to chiprod‐
74 uct(RESIDUE)(nresnr).xvg and their occupancies to histo-chiprod‐
75 uct(RESIDUE)(nresnr).xvg.
76 The option -r generates a contour plot of the average omega angle as a
78 function of the phi and psi angles, that is, in a Ramachandran plot the
79 average omega angle is plotted using color coding.
80
82 Options to specify input files:
83 -s [<.gro/.g96/...>] (conf.gro)
85 Structure file: gro g96 pdb brk ent esp tpr
86 -f [<.xtc/.trr/...>] (traj.xtc)
88 Trajectory: xtc trr cpt gro g96 pdb tng
89 -ss [<.dat>] (ssdump.dat) (Optional)
91 Generic data file
92 Options to specify output files:
94 -o [<.xvg>] (order.xvg)
96 xvgr/xmgr file
97 -p [<.pdb>] (order.pdb) (Optional)
99 Protein data bank file
100 -jc [<.xvg>] (Jcoupling.xvg)
102 xvgr/xmgr file
103 -corr [<.xvg>] (dihcorr.xvg) (Optional)
105 xvgr/xmgr file
106 -g [<.log>] (chi.log)
108 Log file
109 -ot [<.xvg>] (dihtrans.xvg) (Optional)
111 xvgr/xmgr file
112 -oh [<.xvg>] (trhisto.xvg) (Optional)
114 xvgr/xmgr file
115 -rt [<.xvg>] (restrans.xvg) (Optional)
117 xvgr/xmgr file
118 -cp [<.xvg>] (chiprodhisto.xvg) (Optional)
120 xvgr/xmgr file
121 Other options:
123 -b <time> (0)
125 Time of first frame to read from trajectory (default unit ps)
126 -e <time> (0)
128 Time of last frame to read from trajectory (default unit ps)
129 -dt <time> (0)
131 Only use frame when t MOD dt = first time (default unit ps)
132 -[no]w (no)
134 View output .xvg, .xpm, .eps and .pdb files
135 -xvg <enum> (xmgrace)
137 xvg plot formatting: xmgrace, xmgr, none
138 -r0 <int> (1)
140 starting residue
141 -[no]phi (no)
143 Output for phi dihedral angles
144 -[no]psi (no)
146 Output for psi dihedral angles
147 -[no]omega (no)
149 Output for omega dihedrals (peptide bonds)
150 -[no]rama (no)
152 Generate phi/psi and chi_1/chi_2 Ramachandran plots
153 -[no]viol (no)
155 Write a file that gives 0 or 1 for violated Ramachandran angles
156 -[no]periodic (yes)
158 Print dihedral angles modulo 360 degrees
159 -[no]all (no)
161 Output separate files for every dihedral.
162 -[no]rad (no)
164 in angle vs time files, use radians rather than degrees.
165 -[no]shift (no)
167 Compute chemical shifts from phi/psi angles
168 -binwidth <int> (1)
170 bin width for histograms (degrees)
171 -core_rotamer <real> (0.5)
173 only the central -core_rotamer*(360/multiplicity) belongs to
174 each rotamer (the rest is assigned to rotamer 0)
175 -maxchi <enum> (0)
177 calculate first ndih chi dihedrals: 0, 1, 2, 3, 4, 5, 6
178 -[no]normhisto (yes)
180 Normalize histograms
181 -[no]ramomega (no)
183 compute average omega as a function of phi/psi and plot it in an
184 .xpm plot
185 -bfact <real> (-1)
187 B-factor value for .pdb file for atoms with no calculated dihe‐
188 dral order parameter
189 -[no]chi_prod (no)
191 compute a single cumulative rotamer for each residue
192 -[no]HChi (no)
194 Include dihedrals to sidechain hydrogens
195 -bmax <real> (0)
197 Maximum B-factor on any of the atoms that make up a dihedral,
198 for the dihedral angle to be considere in the statistics. Ap‐
199 plies to database work where a number of X-Ray structures is an‐
200 alyzed. -bmax <= 0 means no limit.
201 -acflen <int> (-1)
203 Length of the ACF, default is half the number of frames
204 -[no]normalize (yes)
206 Normalize ACF
207 -P <enum> (0)
209 Order of Legendre polynomial for ACF (0 indicates none): 0, 1,
210 2, 3
211 -fitfn <enum> (none)
213 Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
214 -beginfit <real> (0)
216 Time where to begin the exponential fit of the correlation func‐
217 tion
218 -endfit <real> (-1)
220 Time where to end the exponential fit of the correlation func‐
221 tion, -1 is until the end
222
224 • Produces MANY output files (up to about 4 times the number of
225 residues in the protein, twice that if autocorrelation functions are
226 calculated). Typically several hundred files are output.
227 • phi and psi dihedrals are calculated in a non-standard way, using
229 H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead
230 of N-CA-C-N(+). This causes (usually small) discrepancies with the
231 output of other tools like gmx rama.
232 • -r0 option does not work properly
234 • Rotamers with multiplicity 2 are printed in chi.log as if they had
236 • multiplicity 3, with the 3rd (g(+)) always having probability 0
238
240 gmx(1)
241 More information about GROMACS is available at <‐
243 http://www.gromacs.org/>.
244
246 2022, GROMACS development team
2472022.3 Sep 02, 2022 GMX-CHI(1)