1GMX-CHI(1)                          GROMACS                         GMX-CHI(1)
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3
4

NAME

6       gmx-chi - Calculate everything you want to know about chi and other di‐
7       hedrals
8

SYNOPSIS

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

DESCRIPTION

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
29       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
37       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
41       A log file (argument -g) is also written. This contains
42
43          • information about the number of residues of each type.
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45          • The NMR ^3J coupling constants from the Karplus equation.
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47          • 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
51          • a table for each residue of the rotamer occupancy.
52
53       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
59       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
67       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
77       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

OPTIONS

82       Options to specify input files:
83
84       -s [<.gro/.g96/...>] (conf.gro)
85              Structure file: gro g96 pdb brk ent esp tpr
86
87       -f [<.xtc/.trr/...>] (traj.xtc)
88              Trajectory: xtc trr cpt gro g96 pdb tng
89
90       -ss [<.dat>] (ssdump.dat) (Optional)
91              Generic data file
92
93       Options to specify output files:
94
95       -o [<.xvg>] (order.xvg)
96              xvgr/xmgr file
97
98       -p [<.pdb>] (order.pdb) (Optional)
99              Protein data bank file
100
101       -jc [<.xvg>] (Jcoupling.xvg)
102              xvgr/xmgr file
103
104       -corr [<.xvg>] (dihcorr.xvg) (Optional)
105              xvgr/xmgr file
106
107       -g [<.log>] (chi.log)
108              Log file
109
110       -ot [<.xvg>] (dihtrans.xvg) (Optional)
111              xvgr/xmgr file
112
113       -oh [<.xvg>] (trhisto.xvg) (Optional)
114              xvgr/xmgr file
115
116       -rt [<.xvg>] (restrans.xvg) (Optional)
117              xvgr/xmgr file
118
119       -cp [<.xvg>] (chiprodhisto.xvg) (Optional)
120              xvgr/xmgr file
121
122       Other options:
123
124       -b <time> (0)
125              Time of first frame to read from trajectory (default unit ps)
126
127       -e <time> (0)
128              Time of last frame to read from trajectory (default unit ps)
129
130       -dt <time> (0)
131              Only use frame when t MOD dt = first time (default unit ps)
132
133       -[no]w (no)
134              View output .xvg, .xpm, .eps and .pdb files
135
136       -xvg <enum> (xmgrace)
137              xvg plot formatting: xmgrace, xmgr, none
138
139       -r0 <int> (1)
140              starting residue
141
142       -[no]phi (no)
143              Output for phi dihedral angles
144
145       -[no]psi (no)
146              Output for psi dihedral angles
147
148       -[no]omega (no)
149              Output for omega dihedrals (peptide bonds)
150
151       -[no]rama (no)
152              Generate phi/psi and chi_1/chi_2 Ramachandran plots
153
154       -[no]viol (no)
155              Write a file that gives 0 or 1 for violated Ramachandran angles
156
157       -[no]periodic (yes)
158              Print dihedral angles modulo 360 degrees
159
160       -[no]all (no)
161              Output separate files for every dihedral.
162
163       -[no]rad (no)
164              in angle vs time files, use radians rather than degrees.
165
166       -[no]shift (no)
167              Compute chemical shifts from phi/psi angles
168
169       -binwidth <int> (1)
170              bin width for histograms (degrees)
171
172       -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
176       -maxchi <enum> (0)
177              calculate first ndih chi dihedrals: 0, 1, 2, 3, 4, 5, 6
178
179       -[no]normhisto (yes)
180              Normalize histograms
181
182       -[no]ramomega (no)
183              compute average omega as a function of phi/psi and plot it in an
184              .xpm plot
185
186       -bfact <real> (-1)
187              B-factor value for .pdb file for atoms with no calculated  dihe‐
188              dral order parameter
189
190       -[no]chi_prod (no)
191              compute a single cumulative rotamer for each residue
192
193       -[no]HChi (no)
194              Include dihedrals to sidechain hydrogens
195
196       -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
202       -acflen <int> (-1)
203              Length of the ACF, default is half the number of frames
204
205       -[no]normalize (yes)
206              Normalize ACF
207
208       -P <enum> (0)
209              Order of Legendre polynomial for ACF (0 indicates none):  0,  1,
210              2, 3
211
212       -fitfn <enum> (none)
213              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
214
215       -beginfit <real> (0)
216              Time where to begin the exponential fit of the correlation func‐
217              tion
218
219       -endfit <real> (-1)
220              Time where to end the exponential fit of the  correlation  func‐
221              tion, -1 is until the end
222

KNOWN ISSUES

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
228       • 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
233-r0 option does not work properly
234
235       • Rotamers with multiplicity 2 are printed in chi.log as if they had
236
237       • multiplicity 3, with the 3rd (g(+)) always having probability 0
238

SEE ALSO

240       gmx(1)
241
242       More    information    about    GROMACS    is    available    at     <‐
243       http://www.gromacs.org/>.
244
246       2022, GROMACS development team
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2512022.3                           Sep 02, 2022                       GMX-CHI(1)
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