Ligand desolvation - Revision history

Frodo: asdf

2024-05-25T00:23:46Z

asdf

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

			[[Category:Grids]]
			[[Category:DOCK]]

Frodo at 05:34, 14 February 2014

2014-02-14T05:34:30Z

← Older revision		Revision as of 05:34, 14 February 2014
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	$DOCK6_HOME/bin/solvmap		$DOCK6_HOME/bin/solvmap
	where $DOCK6_HOME refers to the your DOCK6 distribution.		where $DOCK6_HOME refers to the your DOCK6 distribution.

			[[Category:Docking]]

Therese: 4 revisions

2012-10-08T20:29:19Z

4 revisions

← Older revision	Revision as of 20:29, 8 October 2012
(No difference)

Mysinger: /* Creating SOLVMAP grids */

2008-02-06T18:20:39Z

Creating SOLVMAP grids

← Older revision		Revision as of 18:20, 6 February 2008
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	The phimap can then be created by running the executable solvmap in $DOCK6_HOME/bin as:		The phimap can then be created by running the executable solvmap in $DOCK6_HOME/bin as:
	$~~DOCK6/HOME~~/bin/solvmap		$DOCK6_HOME/bin/solvmap
	where $DOCK6_HOME refers to the your DOCK6 distribution.		where $DOCK6_HOME refers to the your DOCK6 distribution.

Mysinger: /* Creating SOLVMAP grids */

2008-02-06T18:20:19Z

Creating SOLVMAP grids

← Older revision		Revision as of 18:20, 6 February 2008
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	#Your protein/receptor in PDB format.		#Your protein/receptor in PDB format.
	#* Example in $DOCK6_HOME/install/test/solvgrid_generation/rec.crg		#* Example in $DOCK6_HOME/install/test/solvgrid_generation/rec.crg
	#Bounding box		#Bounding box for the grid
	#* Example in $DOCK6_HOME/install/test/solvgrid_generation/box		#* Example in $DOCK6_HOME/install/test/solvgrid_generation/box

Mysinger: /* Creating SOLVMAP grids */

2008-02-06T18:19:57Z

Creating SOLVMAP grids

New page

Ligand desolvation is calculated as a part of the dock3.5 score as implemented in DOCK 6. There are two options to calculate ligand desolvation: full and volume based. Atomic desolvation for each atom in the ligand is calculated using [http://comp.chem.umn.edu/amsol/ AMSOL]. Full desolvation is calculated as a sum over atomic desolvation. Volume based desolvation is calculated by multiplying the atomic desolvation by a normalization factor that accounts for the burial of the ligand atom in the binding site. 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. This calculated by the program solvmap distributed with DOCK 6. For more information please see the [http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm DOCK6 manual].

=== Creating SOLVMAP grids ===

To create a SOLVMAP you will need:
#Input instructions in a local INSOLV file
#* Example in $DOCK6_HOME/install/test/solvgrid_generation/INSOLV
#Your protein/receptor in PDB format.
#* Example in $DOCK6_HOME/install/test/solvgrid_generation/rec.crg
#Bounding box
#* Example in $DOCK6_HOME/install/test/solvgrid_generation/box

The phimap can then be created by running the executable solvmap in $DOCK6_HOME/bin as:
$DOCK6/HOME/bin/solvmap
where $DOCK6_HOME refers to the your DOCK6 distribution.