1GMX-CHI(1)                          GROMACS                         GMX-CHI(1)
2
3
4

NAME

6       gmx-chi  -  Calculate  everything  you want to know about chi and other
7       dihedrals
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,
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
38       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
42       A log file (argument -g) is also written. This contains
43
44          · information about the number of residues of each type.
45
46          · The NMR ^3J coupling constants from the Karplus equation.
47
48          · 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
52          · a table for each residue of the rotamer occupancy.
53
54       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
60       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
68       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
78       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

OPTIONS

83       Options to specify input files:
84
85       -s [<.gro/.g96/…>] (conf.gro)
86              Structure file: gro g96 pdb brk ent esp tpr
87
88       -f [<.xtc/.trr/…>] (traj.xtc)
89              Trajectory: xtc trr cpt gro g96 pdb tng
90
91       -ss [<.dat>] (ssdump.dat) (Optional)
92              Generic data file
93
94       Options to specify output files:
95
96       -o [<.xvg>] (order.xvg)
97              xvgr/xmgr file
98
99       -p [<.pdb>] (order.pdb) (Optional)
100              Protein data bank file
101
102       -jc [<.xvg>] (Jcoupling.xvg)
103              xvgr/xmgr file
104
105       -corr [<.xvg>] (dihcorr.xvg) (Optional)
106              xvgr/xmgr file
107
108       -g [<.log>] (chi.log)
109              Log file
110
111       -ot [<.xvg>] (dihtrans.xvg) (Optional)
112              xvgr/xmgr file
113
114       -oh [<.xvg>] (trhisto.xvg) (Optional)
115              xvgr/xmgr file
116
117       -rt [<.xvg>] (restrans.xvg) (Optional)
118              xvgr/xmgr file
119
120       -cp [<.xvg>] (chiprodhisto.xvg) (Optional)
121              xvgr/xmgr file
122
123       Other options:
124
125       -b <time> (0)
126              Time of first frame to read from trajectory (default unit ps)
127
128       -e <time> (0)
129              Time of last frame to read from trajectory (default unit ps)
130
131       -dt <time> (0)
132              Only use frame when t MOD dt = first time (default unit ps)
133
134       -[no]w (no)
135              View output .xvg, .xpm, .eps and .pdb files
136
137       -xvg <enum> (xmgrace)
138              xvg plot formatting: xmgrace, xmgr, none
139
140       -r0 <int> (1)
141              starting residue
142
143       -[no]phi (no)
144              Output for phi dihedral angles
145
146       -[no]psi (no)
147              Output for psi dihedral angles
148
149       -[no]omega (no)
150              Output for omega dihedrals (peptide bonds)
151
152       -[no]rama (no)
153              Generate phi/psi and chi_1/chi_2 Ramachandran plots
154
155       -[no]viol (no)
156              Write a file that gives 0 or 1 for violated Ramachandran angles
157
158       -[no]periodic (yes)
159              Print dihedral angles modulo 360 degrees
160
161       -[no]all (no)
162              Output separate files for every dihedral.
163
164       -[no]rad (no)
165              in angle vs time files, use radians rather than degrees.
166
167       -[no]shift (no)
168              Compute chemical shifts from phi/psi angles
169
170       -binwidth <int> (1)
171              bin width for histograms (degrees)
172
173       -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
177       -maxchi <enum> (0)
178              calculate first ndih chi dihedrals: 0, 1, 2, 3, 4, 5, 6
179
180       -[no]normhisto (yes)
181              Normalize histograms
182
183       -[no]ramomega (no)
184              compute average omega as a function of phi/psi and plot it in an
185              .xpm plot
186
187       -bfact <real> (-1)
188              B-factor  value for .pdb file for atoms with no calculated dihe‐
189              dral order parameter
190
191       -[no]chi_prod (no)
192              compute a single cumulative rotamer for each residue
193
194       -[no]HChi (no)
195              Include dihedrals to sidechain hydrogens
196
197       -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
203       -acflen <int> (-1)
204              Length of the ACF, default is half the number of frames
205
206       -[no]normalize (yes)
207              Normalize ACF
208
209       -P <enum> (0)
210              Order  of  Legendre polynomial for ACF (0 indicates none): 0, 1,
211              2, 3
212
213       -fitfn <enum> (none)
214              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
215
216       -beginfit <real> (0)
217              Time where to begin the exponential fit of the correlation func‐
218              tion
219
220       -endfit <real> (-1)
221              Time  where  to end the exponential fit of the correlation func‐
222              tion, -1 is until the end
223

KNOWN ISSUES

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
229       · 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
234       · -r0 option does not work properly
235
236       · 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

SEE ALSO

240       gmx(1)
241
242       More    information    about    GROMACS    is    available    at     <‐
243       http://www.gromacs.org/>.
244
246       2019, GROMACS development team
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2512019.4                           Oct 02, 2019                       GMX-CHI(1)
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