z-Matrix and Internal Coordinates

  z-Matrix and Internal Coordinates
************************************************************
** Setting up the cyclohexane structure using a z-matrix
****** The System *******************************************
spectrometer(MHz)  *
spinning_freq(kHz) *
channels           H1
nuclei             H1
atomic_coords      *
cs_isotropic       *
csa_parameters     *
j_coupling         *
quadrupole         *
dip_switchboard    *
csa_switchboard    *
exchange_nuclei    *
bond_len_nuclei    (1 7)
bond_ang_nuclei    (1 2 3)
tors_ang_nuclei    (1 2 3 4)
groups_nuclei      *
******* Pulse Sequence ****
CHN 1
timing(usec)       0
power(kHz)         0 
phase(deg)         0  
freq_offs(kHz)     0  
****** Variables **********
rCC=1.5
rCH=1
theta=109.4712
******* Options ***********
rho0               I1x
observables        I1x
EulerAngles        *
n_gamma            *
line_broaden(Hz)   *
zerofill           *
FFT_dimensions     *
options            -zxmatzxmat.dat -s -expcm

* The atomic coordinates of the structure created via a z-matrix or
  internal variables can be inspected with the -s option
* The coordinates can be used to draw the strucure
  in molecular/crystal graphics programs (e.g., CrystalMaker,
  see the cyclohexane.pdf file)
* -s -expcm: export coordinates in a format readable by Crystal Maker
* The internal coordinates r_1, phi_1, and theta_1 are defined at the
  bond_len_nuclei, bond_ang_nuclei, and tors_ang_nuclei lines but they
  are not set in the Variables section. So, they are only measured, and
  can be inspected (in the -s option printout) to verify that the molecule
  was generated correctly
zxmat.dat
C13 1  
C13 2   1  rCC 
C13 3   2  rCC  1  theta  
C13 4   3  rCC  2  theta  1   60
C13 5   4  rCC  3  theta  2  -60
C13 6   5  rCC  4  theta  3   60
H1  7   1  rCH  2  theta  3   60
H1  8   1  rCH  2  theta  3  180
H1  9   2  rCH  3  theta  4  -60
H1  10  2  rCH  3  theta  4  180
H1  11  3  rCH  4  theta  5   60
H1  12  3  rCH  4  theta  5  180
H1  13  4  rCH  5  theta  6  -60
H1  14  4  rCH  5  theta  6  180
H1  15  5  rCH  6  theta  1   60
H1  16  5  rCH  6  theta  1  180
H1  17  6  rCH  1  theta  2  -60
H1  18  6  rCH  1  theta  2  180