topology {<topology-statement>} end

<topology-statement> :==

  mass <type> <real>
  --{Atom type and default mass.}
  residue <resname> {<residue-specification>} end
  --{Define the topology of a residue.}
  presidue <resname> {delete|add|modify|omit <residue-specification>} end
  --{Define the topology of a patch residue.}
  autogenerate [angle=<logical>] [dihedral=<logical>] end
  --{Enable autogeneration of angle and dihedral topology
     entries based on bond list. This is not active for patch
     residue, thus angles and dihedrals must be explicitly defined.}
  reset
  --{Ignore all previous entries into topology database.}
  ?
  --{Print current topology database.}

  <residue-specification> :==

    atom [<reference>]<atom> {<atom-specification>} end
    --{Define an atom in the residue.}
    bond [<reference>]<atom> [<reference>]<atom>
    --{Define a pair of atoms in the residue which are connected by a bond.}
    angle [<reference>]<atom> [<reference>]<atom> [<reference>]<atom>
    --{Define a triple of atoms in the residue which are connected by 2 bonds.}
    dihedral [<reference>]<atom> [<reference>]<atom> 
             [<reference>]<atom> [<reference>]<atom> [multiplicy <integer>]
    --{Define a quadruple of atoms in the residue which form a torsion
       angle around a common central bond.}
    improper [<reference>]<atom> [<reference>]<atom> 
             [<reference>]<atom> [<reference>]<atom> [multiplicy <integer>]
    --{Define a quadruple of atoms in the residue which will be treated as
       if there is a bond between the centre 2 atoms.}
    donor [<reference>]<atom> [<reference>]<atom>
    --{Define a hydrogen bond donor. Hydrogen atom followed by connected
       heavy atom.}
    acceptor [<reference>]<atom> [<reference>]<atom>|none
    --{Define a hydrogen bond acceptor. Bond acceptor followed by optional
       connected heavy atom.}

    <atom-specification> :==

      type=<type>
      --{Type of this atom.}
      charge=<real>
      --{Charge of this atom.}
      mass=<real>
      --{Mass of this atom.}
      exclude=( {[<reference>]<atom>} )
      --{Exclude the following atoms from interactions with this atom.}

    --{The <reference> character is only required for patch residues.}