The atom typing is centred to the assumption that atoms in analogous chemical environment will usually have local properties that are transferable between molecules. This concept plays a pivotal role not only in the parameterization of the potential energy functions (force field), but also in the calculation of all molecular properties based on an atomic parametrization (e.g. logP prediction).

For this reason we sought a method able to describe the atom typing of both force fields and atomic parametrizations. We here propose ATDL language that is able to define any atom type and it makes possible to change from one atom type classification to another, referring to the corresponding ATDL definition.

Each atom is defined by a five-character string. The first two characters are the element symbol of atom. If the element symbol is one character only, the second character must be a dash (-). For a better description, special elements are included: X for any atom and # for any heavy atom. The third character is the bond order: one can use values from 1 to 6 for real bond order, 0 for non bonded atom and 9 for a bonded atom without specified bond order. The fourth character is the ring indicator: ranging from 3 to 6 if the atom is a 3 to 6-ring member, 0 for a non-ring member atom and 9 for a non-specified ring atom. The fifth character is the aromatic indicator: 0 for non-aromatic atom, 1 for aromatic atom and 9 if the aromaticity is non-specified.

Examples:
C-300 is a sp² aliphatic carbon, Si900 is a generic silicon with any bonds order and C-361 is an aromatic carbon included in a six-member ring.

After the atom definition you can write the description of bonded atoms (also in ATDL) limited by parenthesis as the description of connected atoms is crucial to correctly define the atom properties. For example O-200 indicates an oxygen atom not involved in a ring bonded to two other atoms. This specification can be used both for an hydroxyl group and for an ether function. In order to resolve this disagreement you can point out the description of connected atom in ATDL: O-200 (C-400 H-100) for hydroxyl group and O-200 (C-400 C-400) for ether.

More than one level of parenthesis can be used for complex description of atom types and each group of atoms, limited by parenthesis, contains the descriptions of all atoms bonded to the previous atom.

C-400 (N-400 (H-100 H-100 H-100) C-300 (O-100 O-100) H-100 H-100)

In this way you can indicate a sp³ carbon bonded to two hydrogen atoms (H-100), a nitrogen atom positively charged (N-400) with three hydrogen atoms and a sp² carbon bonded to two oxygen atoms non substituted.

With ATDL specifications it’s virtually possible define any atom type describing all bonded atoms until giving a representation of whole molecule.

For each atom typing scheme (force field or atomic parametrization) VEGA uses a template file, in which the descriptions of atom types are stored along with a symbolic code (for force fields) or a local value (for atomic contributions). Each atom type definition is stored in a line with three columns. The first column is the atom type name (or value), the second column is the atom description in ATDL and the third column contains the descriptions of bonded atoms (also in ATDL).