# ----------------------------------------------------------------------
  # --   General comment:                                               --
  # -- The write() and write_once() commands create and append text to  --
  # -- files (replacing variables beginning with @ or $ with counters.) --
  # -- File names beginning with "In " or "Data " are special.          --
  # -- They will be pasted into the LAMMPS input script and             --
  # -- data files which are generated by moltemplate.  The syntax       --
  # -- of these files is exactly the same as the syntax from the        --
  # -- corresponding sections of a LAMMPS input script or data file.    --
  # ----------------------------------------------------------------------


Monomer {

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

  write("Data Atoms") {
    $atom:CA $mol:... @atom:CA    0.0   0.000  0.4000  0.00000
    $atom:R1 $mol:... @atom:R     0.0   0.000  1.000   1.000
    $atom:R2 $mol:... @atom:R     0.0   0.000  1.000  -1.000
  }

  #  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


  # atom-type  mass

  write_once("Data Masses") {
    @atom:CA   13.0
    @atom:R    50.0
  }

  #        atom-type   atom-type   epsilon sigma

  write_once("In Settings") {
    pair_coeff @atom:CA @atom:CA    0.05   2.0
    pair_coeff @atom:R  @atom:R     0.50   2.0
  }

  # bond-id   bond-type        atom-id1  atom-id2

  write("Data Bonds") {
    $bond:CR1  @bond:sidechain  $atom:CA  $atom:R1
    $bond:CR2  @bond:sidechain  $atom:CA  $atom:R2
  }

  write_once("In Settings") {
    #           bond-type          k     r0
    bond_coeff  @bond:sidechain   30.0   1.2
    bond_coeff  @bond:bb          30.0   2.0    # "bb" shorthand for "backbone"
  }

  # For a compound molecule consisting of smaller building blocks (such as a
  # polymer built from monomers), it is tedious to explicitly list all of the
  # angles, dihedrals in the entire molecule.  Instead, you can define rules
  # for automatically generating all the angular interactions between bonded 
  # atoms according to their connectivity and the atom/bond type.
  # Later, when you connect multiple monomers together to form a polymer, 
  # appropriate bond-angle forces will be applied to these atoms automatically
  # (as well as dihedral and improper forces, if defined).

  #  Rules for determining 3 and 4-body bonded interactions by type

  # angle-type       atomType1 atomType2 atomType3  bondType1 bondType2

  write_once("Data Angles By Type") {
    @angle:backbone  @atom:CA @atom:CA @atom:CA   @bond:*   @bond:*
    @angle:sidechain @atom:CA @atom:CA @atom:R    @bond:*   @bond:*
    @angle:RCR       @atom:R  @atom:CA @atom:R    @bond:*   @bond:*
  }

  # ("@angle:RCR" defines the angle between the R-C-R atoms within a monomer.
  #  The other angular interactions are between atoms in neighboring monomers.)


  # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3

  write_once("Data Dihedrals By Type") {
    @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:*
  }

  # Parameters for these new angular interactions must be defined. (I recommend 
  # putting all force-field parameters (coeffs) in the "In Settings" section.)

  write_once("In Settings") {
    #            angle-type         k    theta0
    angle_coeff  @angle:backbone   50.00  160
    angle_coeff  @angle:sidechain  50.00  120
    angle_coeff  @angle:RCR        50.00  120
    #                  dihedral-type      K1      K2      K3      K4
    dihedral_coeff  @dihedral:backbn  1.411036 -0.271016 3.145034 0.0
  }

} # Monomer






# -------------------------------------------------------------------------
#                            Heteropolymers:
#
# There is a similar example for heteropolymers which is distributed online
# bundled with the moltemplate software.  It is named "2bead_heteropolymer",
# and it demonstrates how to share backbone (CA) atoms, bonds and angles
# (so that you don't have to define them seperately for each type of monomer).
# -------------------------------------------------------------------------