Vdw.defn - Revision history

Frodo at 17:49, 15 February 2014

2014-02-15T17:49:03Z

← Older revision		Revision as of 17:49, 15 February 2014
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	definition C. ( 3 H )		definition C. ( 3 H )
	_____________________________________		_____________________________________


			[[Category:DOCK 6]]

Therese: 3 revisions

2012-10-08T20:33:15Z

3 revisions

← Older revision

Revision as of 20:33, 8 October 2012

Rgc: formatting

2010-03-17T01:40:07Z

formatting

← Older revision		Revision as of 01:40, 17 March 2010
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	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.		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.		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.		WARNING: The last entry in the vdw.defn file MUST be Dummy.

	Sample Entries		Sample Entries

JohnIrwin at 22:57, 19 September 2006

2006-09-19T22:57:51Z

← Older revision		Revision as of 22:57, 19 September 2006
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	WARNING: The last entry in the vdw.defn file MUST be Dummy.		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 )
			_____________________________________

JohnIrwin at 22:57, 19 September 2006

2006-09-19T22:57:34Z

New page

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.