Introduction

The parameter files contain atom and bond data needed during dock calculations. The definition (*.defn) files contain atom and bond labeling data. The table (*.tbl) files contain additional data for chemical interactions and flexible bond torsion positions. They may be edited by the user.

Atom definition rules

The definition files use a consistent atom labeling convention for which an atom in virtually any chemical environment can be identified. The specification of adjacent atoms is nested using the elements listed in Table 7. Some sample definitions are provided in Table 8.

• Each element must be separated by a space.
• If more than one adjacent atom is specified, then ALL must be present (i.e. a boolean AND for rules within a line).
• If a label can have multiple definition lines, then any ONE of them must be satisfied for inclusion (i.e. a boolean OR for rules on different lines).

Table 7. Atom definition elements

element	function
atom type	Specifies partial or complete atom type. A partial specification is more general (i.e. "C" versus "C.3"). An asterisk (*) specifies ANY atom type.
( )	Specifies atoms that must be bonded to parent atom.
[ ]	Specifies atoms that must NOT be bonded to parent atom.
integer	Specifies the number of an atom that must be bonded.

Table 8. Example definitions

example	explanation
C.2 ( 2 O.co2 )	A carboxylate carbon.
.3 [ 3 H ]	Any sp3 hybridized atom that is not attached to three hydrogens.
C. [ O. ] [ N. [ 2 O.2 ] [ 2 C. ] ]	Any carbon not attached to an oxygen or a nitrogen (unless the nitrogen is a nitro or tertiary nitrogen).