Jump to: navigation, search

This file contains atom labels and definitions for van der Waals (VDW) atom typing. The following data types are associated with each atom: VDW radius, VDW well-depth, flag for heavy atom, and valence. The VDW radius and VDW well-depth values are used in molecular mechanics-scoring functions (see Grid). The valence is the value for the maximum number of atoms that can be attached. The definition is the Sybyl atom types that should be associated with the atom name. A label may have multiple definitions.

In the vdw_AMBER_parm99.defn file, there are additional parameters needed for use with the Hawkins GB/SA scoring function (see Hawkins GB/SA). Each entry has an additional gbraii and gbscale parameter.

WARNING: The last entry in the vdw.defn file MUST be Dummy.

Sample Entries

                   name Carbon_sp/sp2
                   atom_model either
                   radius 1.850
                   well_depth 0.120
                   heavy_flag 1
                   valence 4
                   definition C
                   name Carbon_All_sp3
                   atom_model all
                   radius 1.800
                   well_depth 0.060
                   heavy_flag 1
                   valence 4
                   gbradii 1.70
                   gbscale 0.72
                   definition C.3
                   name Carbon_United_CH3
                   atom_model united
                   radius 2.000
                   well_depth 0.150
                   heavy_flag 1
                   valence 4
                   definition C. ( 3 H )