import "alkanes.lt"   # <-- Defines the atoms and force-field used for Alkanes


CH2 inherits Alkanes {

  # atom-id  mol-id atom-type  charge    x        y              z

  write("Data Atoms") {
    $atom:C  $mol:... @atom:c3 -0.120  0.000  0.000             0.000
    $atom:H1 $mol:... @atom:h1  0.060  0.000  0.63104384422426  0.892430762954
    $atom:H2 $mol:... @atom:h1  0.060  0.000  0.63104384422426 -0.892430762954
  }

  #  Note: The "..." in "$mol:..." tells moltemplate that this molecule may
  #        be a part of a larger molecule, and (if so) to use the larger
  #        parent object's molecule id number as it's own.
  #        The CH2 group is part of the Hexadecane molecule.

  # Now specify which pairs of atoms are bonded:
  # bond-id   bond-type   atom-id1  atom-id2

  write('Data Bonds') {
    $bond:b1 @bond:CH  $atom:C $atom:H1
    $bond:b2 @bond:CH  $atom:C $atom:H2
  }

} # CH2




# Atom charges for this example were taken from the OPLSAA force field file:
# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
#
######### (scratchwork calculations for the atomic coordinates) #########
# Lcc = 1.5350 # length of the C-C bond (Sp3)
# Lch = 1.0930 # length of the C-H bond
# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
# DeltaXc = Lcc*sin(theta/2)  # = 1.2533222517240594
# DeltaYc = Lcc*cos(theta/2)  # = 0.8862326632060754
#                             # 0.5*DeltaYc = 0.4431163316030377
# DeltaZh = Lch*sin(theta/2)  # = 0.8924307629540046
# DeltaYh = Lch*cos(theta/2)  # = 0.6310438442242609