Delphi electrostatics - Revision history

Frodo: asdf

2024-05-25T00:22:30Z

asdf

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	[[Category:Software]]		[[Category:Software]]
	[[Category:Electrostatics]]		[[Category:Electrostatics]]

			[[Category:Jargon]]
			[[Category:Scoring]]
			[[Category:Grids]]

Frodo at 04:20, 13 March 2014

2014-03-13T04:20:53Z

← Older revision		Revision as of 04:20, 13 March 2014
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	--[[User:kaushik.raha@gmail.com\|Kaushik]] 09:08, 15 October 2006 (PDT)		--[[User:kaushik.raha@gmail.com\|Kaushik]] 09:08, 15 October 2006 (PDT)


	~~[[Category:DOCK:Scoring problem]]~~
	[[Category:Software]]		[[Category:Software]]
	[[Category:Electrostatics]]		[[Category:Electrostatics]]

Therese: 27 revisions

2012-10-08T20:11:53Z

27 revisions

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Revision as of 20:11, 8 October 2012

Rgc at 22:08, 26 September 2011

2011-09-26T22:08:20Z

← Older revision		Revision as of 22:08, 26 September 2011
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	$DOCK6_HOME/bin/make_phimap $DELPHI_PATH		$DOCK6_HOME/bin/make_phimap $DELPHI_PATH
	$DOCK6_HOME refers to the your DOCK6 distribution and $DELPHI_PATH refers is the path of your DelPhi distribution		$DOCK6_HOME refers to the your DOCK6 distribution and $DELPHI_PATH refers is the path of your DelPhi distribution


			== Visualizing DelPhi grids ==

			[[Visualizing_delphi]]

	--[[User:kaushik.raha@gmail.com\|Kaushik]] 09:08, 15 October 2006 (PDT)		--[[User:kaushik.raha@gmail.com\|Kaushik]] 09:08, 15 October 2006 (PDT)

Mysinger: /* Creating DelPhi electrostatic grids */

2008-02-06T18:21:06Z

Creating DelPhi electrostatic grids

← Older revision		Revision as of 18:21, 6 February 2008
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	The phimap can then be created by running the script make_phimap in $DOCK6_HOME/bin as:		The phimap can then be created by running the script make_phimap in $DOCK6_HOME/bin as:
	$~~DOCK6/HOME~~/bin/make_phimap $DELPHI_PATH		$DOCK6_HOME/bin/make_phimap $DELPHI_PATH
	$DOCK6_HOME refers to the your DOCK6 distribution and $DELPHI_PATH refers is the path of your DelPhi distribution		$DOCK6_HOME refers to the your DOCK6 distribution and $DELPHI_PATH refers is the path of your DelPhi distribution

Mysinger: /* Creating DelPhi electrostatic grids */

2008-02-06T18:11:46Z

Creating DelPhi electrostatic grids

← Older revision		Revision as of 18:11, 6 February 2008
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	To create a DelPhi electrostatic grid (phimap) you will need:		To create a DelPhi electrostatic grid (phimap) you will need:
	#[http://trantor.bioc.columbia.edu/delphi The DelPhi program]		#[http://trantor.bioc.columbia.edu/delphi The DelPhi program]
	#Your protein/receptor in PDB format.		#Your protein/receptor in PDB format with delphi spheres added.
	#* Example in $DOCK6_HOME/install/test/chemgrid_generation/rec+sph.crg		#* Example in $DOCK6_HOME/install/test/chemgrid_generation/rec+sph.crg
	#Atomic charges		#Atomic charges

JohnIrwin at 17:55, 21 September 2007

2007-09-21T17:55:59Z

New page

The program chemgrid produces values for computing force field scores and bump checking. The force field scores, or molecular mechanics interaction energies are calculated as van der Waals and electrostatic components and stored on grids. However only the steric interaction energy grids are used in DOCK 6 as a part of Dock3.5 Score. For calculating the electrostatic interaction, the electrostatic potential of the receptor calculated using the linearized form of Poisson-Boltzmann equation. And electrostatic interaction energy between the ligand and the receptor is calculated from this grid. For more information please see the [http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm DOCK6 manual].

=== Creating DelPhi electrostatic grids ===

To create a DelPhi electrostatic grid (phimap) you will need:
#[http://trantor.bioc.columbia.edu/delphi The DelPhi program]
#Your protein/receptor in PDB format.
#* Example in $DOCK6_HOME/install/test/chemgrid_generation/rec+sph.crg
#Atomic charges
#* Example in $DOCK6_HOME/install/test/chemgrid_generation/amb.crg.oxt
#Atomic radii
#* Example in $DOCK6_HOME/install/test/chemgrid_generation/vdw.siz
#Parameters for running the calculation
#* Example in $DOCK6_HOME/install/test/chemgrid_generation/generic.prm

The phimap can then be created by running the script make_phimap in $DOCK6_HOME/bin as:
$DOCK6/HOME/bin/make_phimap $DELPHI_PATH
$DOCK6_HOME refers to the your DOCK6 distribution and $DELPHI_PATH refers is the path of your DelPhi distribution

--[[User:kaushik.raha@gmail.com|Kaushik]] 09:08, 15 October 2006 (PDT)

[[Category:DOCK:Scoring problem]]
[[Category:Software]]
[[Category:Electrostatics]]