Solvmap - Revision history

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2024-05-25T00:26:39Z

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	[[Category:Docking]]		[[Category:Docking]]
	[[Category:Desolvation]]		[[Category:Desolvation]]
			[[Category:Grids]]

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			[[Category:Desolvation]]

Frodo at 04:25, 14 February 2014

2014-02-14T04:25:29Z

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	~~3.2.2~~ SOLVMAP		SOLVMAP

	AUTHOR: Brian K. Shoichet		AUTHOR: Brian K. Shoichet
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	The solvmap program calculates the grid that is used by DOCK6 for calculating ligand desolvation. Ligand desolvation is calculated as a sum of the atomic desolvation multiplied by a normalization factor that accounts for the extent to which the ligand atom is buried by the binding site. The atomic desolvation for each ligand atom can be calculated by AMSOL (AMSOL is not distributed by us, please follow the link for more information) and is stored in the input file (see file formats). The cost of desolvating each atom, or the normalization factor, is the distance weighted high dielectric volume displaced by the protein that is stored for each grid element in the active site. Thus the volume based ligand desolvation energy is calculated as:		The solvmap program calculates the grid that is used by DOCK6 for calculating ligand desolvation. Ligand desolvation is calculated as a sum of the atomic desolvation multiplied by a normalization factor that accounts for the extent to which the ligand atom is buried by the binding site. The atomic desolvation for each ligand atom can be calculated by AMSOL (AMSOL is not distributed by us, please follow the link for more information) and is stored in the input file (see file formats). The cost of desolvating each atom, or the normalization factor, is the distance weighted high dielectric volume displaced by the protein that is stored for each grid element in the active site. Thus the volume based ligand desolvation energy is calculated as:

	Edesol_equation		Edesol_equation
	Here L is the ligand atom desolvation, volume summed over k volume elements, V. This method is only an approximation to GB solvation and works within the limits of complete burial from the solvent and complete exposure to the solvent on the protein surface. However, being grid-based it is fast and can be used during conformational search and final scoring.		Here L is the ligand atom desolvation, volume summed over k volume elements, V. This method is only an approximation to GB solvation and works within the limits of complete burial from the solvent and complete exposure to the solvent on the protein surface. However, being grid-based it is fast and can be used during conformational search and final scoring.

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	* OUTSOLV #restatement of input parameters; messages pertaining to calculation of the grids		* OUTSOLV #restatement of input parameters; messages pertaining to calculation of the grids
	* solvmap #ligand desolvation grids		* solvmap #ligand desolvation grids

			[[Category:Software]]
			[[Category:Docking]]

Therese: 1 revision

2012-10-08T20:32:24Z

1 revision

← Older revision	Revision as of 20:32, 8 October 2012
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JohnIrwin at 23:02, 19 September 2006

2006-09-19T23:02:02Z

New page

3.2.2 SOLVMAP

AUTHOR: Brian K. Shoichet

DESCRIPTION:

The solvmap program calculates the grid that is used by DOCK6 for calculating ligand desolvation. Ligand desolvation is calculated as a sum of the atomic desolvation multiplied by a normalization factor that accounts for the extent to which the ligand atom is buried by the binding site. The atomic desolvation for each ligand atom can be calculated by AMSOL (AMSOL is not distributed by us, please follow the link for more information) and is stored in the input file (see file formats). The cost of desolvating each atom, or the normalization factor, is the distance weighted high dielectric volume displaced by the protein that is stored for each grid element in the active site. Thus the volume based ligand desolvation energy is calculated as:

Edesol_equation
Here L is the ligand atom desolvation, volume summed over k volume elements, V. This method is only an approximation to GB solvation and works within the limits of complete burial from the solvent and complete exposure to the solvent on the protein surface. However, being grid-based it is fast and can be used during conformational search and final scoring.

USAGE: solvmap

INPUT FILE:

This programs require that an INSOLV file be created in the working directory, which contains the parameters to control the program. The INSOLV parameters for chemgrid are detailed below:

receptor.pdb; receptor file
solvmap ; output grid file
1.4,1.3,1.7,2.2,2.2,1.8 ; radii of oxygen, nitrogen, carbon, sulfur, phosphorus, and "other" atoms.
1.4 ; radius of probe
1 ; grid resolution
box.pdb ; box file

OUTPUT FILES:

* OUTSOLV #restatement of input parameters; messages pertaining to calculation of the grids
* solvmap #ligand desolvation grids