Parameter Files

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.

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).

vdw.defn

chem.defn

chem_match.tbl

chem_score.tbl

chem_screen.tbl

flex.defn

flex_drive.tbl

UC Regents 1998
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