1GMX-CHI(1) GROMACS GMX-CHI(1)
2
6 gmx-chi - Calculate everything you want to know about chi and other
7 dihedrals
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,
32 resolves the problem of periodicity. (Van der Spoel & Berendsen
33 (1997), Biophys. J. 72, 2032-2041). Separate files for each dihedral
34 of each residue (corr(dihedral)(RESIDUE)(nresnr).xvg) are output, as
35 well as a file containing the information for all residues (argument of
36 -corr).
37 With option -all, the angles themselves as a function of time for each
39 residue are printed to separate files (dihedral)(RESIDUE)(nresnr).xvg.
40 These can be in radians or degrees.
41 A log file (argument -g) is also written. This contains
43 · information about the number of residues of each type.
45 · The NMR ^3J coupling constants from the Karplus equation.
47 · a table for each residue of the number of transitions between
49 rotamers per nanosecond, and the order parameter S^2 of each
50 dihedral.
51 · a table for each residue of the rotamer occupancy.
53 All rotamers are taken as 3-fold, except for omega and chi dihedrals to
55 planar groups (i.e. chi_2 of aromatics, Asp and Asn; chi_3 of Glu and
56 Gln; and chi_4 of Arg), which are 2-fold. “rotamer 0” means that the
57 dihedral was not in the core region of each rotamer. The width of the
58 core region can be set with -core_rotamer
59 The S^2 order parameters are also output to an .xvg file (argument -o )
61 and optionally as a .pdb file with the S^2 values as B-factor (argument
62 -p). The total number of rotamer transitions per timestep (argument
63 -ot), the number of transitions per rotamer (argument -rt), and the ^3J
64 couplings (argument -jc), can also be written to .xvg files. Note that
65 the analysis of rotamer transitions assumes that the supplied trajec‐
66 tory frames are equally spaced in time.
67 If -chi_prod is set (and -maxchi > 0), cumulative rotamers, e.g.
69 1+9(chi_1-1)+3(chi_2-1)+(chi_3-1) (if the residue has three 3-fold
70 dihedrals and -maxchi >= 3) are calculated. As before, if any dihedral
71 is not in the core region, the rotamer is taken to be 0. The occupan‐
72 cies of these cumulative rotamers (starting with rotamer 0) are written
73 to the file that is the argument of -cp, and if the -all flag is given,
74 the rotamers as functions of time are written to chiprod‐
75 uct(RESIDUE)(nresnr).xvg and their occupancies to histo-chiprod‐
76 uct(RESIDUE)(nresnr).xvg.
77 The option -r generates a contour plot of the average omega angle as a
79 function of the phi and psi angles, that is, in a Ramachandran plot the
80 average omega angle is plotted using color coding.
81
83 Options to specify input files:
84 -s [<.gro/.g96/…>] (conf.gro)
86 Structure file: gro g96 pdb brk ent esp tpr
87 -f [<.xtc/.trr/…>] (traj.xtc)
89 Trajectory: xtc trr cpt gro g96 pdb tng
90 -ss [<.dat>] (ssdump.dat) (Optional)
92 Generic data file
93 Options to specify output files:
95 -o [<.xvg>] (order.xvg)
97 xvgr/xmgr file
98 -p [<.pdb>] (order.pdb) (Optional)
100 Protein data bank file
101 -jc [<.xvg>] (Jcoupling.xvg)
103 xvgr/xmgr file
104 -corr [<.xvg>] (dihcorr.xvg) (Optional)
106 xvgr/xmgr file
107 -g [<.log>] (chi.log)
109 Log file
110 -ot [<.xvg>] (dihtrans.xvg) (Optional)
112 xvgr/xmgr file
113 -oh [<.xvg>] (trhisto.xvg) (Optional)
115 xvgr/xmgr file
116 -rt [<.xvg>] (restrans.xvg) (Optional)
118 xvgr/xmgr file
119 -cp [<.xvg>] (chiprodhisto.xvg) (Optional)
121 xvgr/xmgr file
122 Other options:
124 -b <time> (0)
126 Time of first frame to read from trajectory (default unit ps)
127 -e <time> (0)
129 Time of last frame to read from trajectory (default unit ps)
130 -dt <time> (0)
132 Only use frame when t MOD dt = first time (default unit ps)
133 -[no]w (no)
135 View output .xvg, .xpm, .eps and .pdb files
136 -xvg <enum> (xmgrace)
138 xvg plot formatting: xmgrace, xmgr, none
139 -r0 <int> (1)
141 starting residue
142 -[no]phi (no)
144 Output for phi dihedral angles
145 -[no]psi (no)
147 Output for psi dihedral angles
148 -[no]omega (no)
150 Output for omega dihedrals (peptide bonds)
151 -[no]rama (no)
153 Generate phi/psi and chi_1/chi_2 Ramachandran plots
154 -[no]viol (no)
156 Write a file that gives 0 or 1 for violated Ramachandran angles
157 -[no]periodic (yes)
159 Print dihedral angles modulo 360 degrees
160 -[no]all (no)
162 Output separate files for every dihedral.
163 -[no]rad (no)
165 in angle vs time files, use radians rather than degrees.
166 -[no]shift (no)
168 Compute chemical shifts from phi/psi angles
169 -binwidth <int> (1)
171 bin width for histograms (degrees)
172 -core_rotamer <real> (0.5)
174 only the central -core_rotamer*(360/multiplicity) belongs to
175 each rotamer (the rest is assigned to rotamer 0)
176 -maxchi <enum> (0)
178 calculate first ndih chi dihedrals: 0, 1, 2, 3, 4, 5, 6
179 -[no]normhisto (yes)
181 Normalize histograms
182 -[no]ramomega (no)
184 compute average omega as a function of phi/psi and plot it in an
185 .xpm plot
186 -bfact <real> (-1)
188 B-factor value for .pdb file for atoms with no calculated dihe‐
189 dral order parameter
190 -[no]chi_prod (no)
192 compute a single cumulative rotamer for each residue
193 -[no]HChi (no)
195 Include dihedrals to sidechain hydrogens
196 -bmax <real> (0)
198 Maximum B-factor on any of the atoms that make up a dihedral,
199 for the dihedral angle to be considere in the statistics.
200 Applies to database work where a number of X-Ray structures is
201 analyzed. -bmax <= 0 means no limit.
202 -acflen <int> (-1)
204 Length of the ACF, default is half the number of frames
205 -[no]normalize (yes)
207 Normalize ACF
208 -P <enum> (0)
210 Order of Legendre polynomial for ACF (0 indicates none): 0, 1,
211 2, 3
212 -fitfn <enum> (none)
214 Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
215 -beginfit <real> (0)
217 Time where to begin the exponential fit of the correlation func‐
218 tion
219 -endfit <real> (-1)
221 Time where to end the exponential fit of the correlation func‐
222 tion, -1 is until the end
223
225 · Produces MANY output files (up to about 4 times the number of
226 residues in the protein, twice that if autocorrelation functions are
227 calculated). Typically several hundred files are output.
228 · phi and psi dihedrals are calculated in a non-standard way, using
230 H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead
231 of N-CA-C-N(+). This causes (usually small) discrepancies with the
232 output of other tools like gmx rama.
233 · -r0 option does not work properly
235 · Rotamers with multiplicity 2 are printed in chi.log as if they had
237 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 2019, GROMACS development team
2472018.7 May 29, 2019 GMX-CHI(1)