Blastermaster files - Revision history

Frodo at 15:10, 25 March 2014

2014-03-25T15:10:41Z

← Older revision		Revision as of 15:10, 25 March 2014
Line 91:		Line 91:

	Blastermaster first appeared in [[DOCK 3.7]].		Blastermaster first appeared in [[DOCK 3.7]].
			Return to [[Blastermaster]].

	[[Category:Manual]]		[[Category:Manual]]
	[[Category:DOCK 3.7]]		[[Category:DOCK 3.7]]
	[[Category:Internal]]		[[Category:Internal]]

Frodo at 15:10, 25 March 2014

2014-03-25T15:10:16Z

← Older revision		Revision as of 15:10, 25 March 2014
Line 6:		Line 6:
	{{TOCright}}		{{TOCright}}

	= dockfiles =		= dockfiles directory =

	== posing ==		== posing ==
Line 19:		Line 19:
	* vdw.parms.amb.mindock - atom type lookup table		* vdw.parms.amb.mindock - atom type lookup table

	= working =		= working directory =
	== spheres (hotspots) ==		== spheres (hotspots) ==
	* matching_spheres.log		* matching_spheres.log
Line 38:		Line 38:
	* box		* box

	=== ChemGrid ~~(VDW~~) grids ===		=== VdW (ChemGrid) scoring grids ===
	* OUTCHEM		* OUTCHEM
	* vdw.bmp		* vdw.bmp
Line 50:		Line 50:
	* rec.crg.pdb.dms		* rec.crg.pdb.dms

	=== Electrostatics (qnifft) ===		=== Electrostatics (qnifft) scoring grids ===
	* qnifft.electrostatics.phi		* qnifft.electrostatics.phi
	* qnifft.eps		* qnifft.eps
Line 58:		Line 58:
	* amb.crg.oxt		* amb.crg.oxt
	* trim.electrostatics.phi		* trim.electrostatics.phi


	=== ligand desolvation grids ===		=== ligand desolvation grids ===
Line 65:		Line 64:


	== ~~receptor model~~ ==		== to be sorted ==
	* lowdielectric.sph.pdb		* lowdielectric.sph.pdb


	~~== unsorted ==~~
	* lowdielectric.sph.pdb.log		* lowdielectric.sph.pdb.log
	* filter.log		* filter.log

Frodo: /* dockfiles */

2014-03-25T15:08:44Z

dockfiles

← Older revision		Revision as of 15:08, 25 March 2014
Line 7:		Line 7:

	= dockfiles =		= dockfiles =
	* ligand.desolv.heavy
	* matching_spheres.sph		== posing ==
	* vdw.bmp		* matching_spheres.sph - spheres (hotspots)
	* ~~vdw~~.~~vdw~~		* vdw.bmp - bump map to rapidly eliminate unproductive poses
	* ligand.desolv.hydrogen
	* trim.electrostatics.phi		== scoring ==
	* vdw.parms.amb.mindock		* ligand.desolv.heavy - ligand desolvation scoring grid, non-H atoms
			* ligand.desolv.hydrogen - ligand desolvation scoring grid, H atoms
			* trim.electrostatics.phi - electrostatics scoring grid
			* vdw.vdw - van der Waals scoring grid
			* vdw.parms.amb.mindock - atom type lookup table

	= working =		= working =

Frodo at 15:03, 25 March 2014

2014-03-25T15:03:45Z

← Older revision		Revision as of 15:03, 25 March 2014
Line 1:		Line 1:
	Meaning of the files created by Blastermaster.		Meaning of the files created by Blastermaster.
	These are also documented with each associated program, but since [[Blastermaster]] is the widely used interface for docking, they are collected and organized here.		These are also documented with each associated program, but since [[Blastermaster]] is the widely used interface for docking, they are collected and organized here.

			Blastermaster creates files in two directories, working and dockfiles. Only dockfiles is necessary for running DOCK 3.7. working contains intermediate files used in the preparation of the final dockfiles for docking.

	{{TOCright}}		{{TOCright}}

	= ~~Files for~~ spheres (~~hot spots~~) =		= dockfiles =
			* ligand.desolv.heavy
			* matching_spheres.sph
			* vdw.bmp
			* vdw.vdw
			* ligand.desolv.hydrogen
			* trim.electrostatics.phi
			* vdw.parms.amb.mindock

			= working =
			== spheres (hotspots) ==
	* matching_spheres.log		* matching_spheres.log
	* matching_spheres.sph		* matching_spheres.sph
Line 13:		Line 25:
	* vdw.siz		* vdw.siz

			== protonation ==
	= ~~receptor~~ protonation =
	* addh.log		* addh.log
	* reduce_wwPDB_het_dict.txt		* reduce_wwPDB_het_dict.txt

			== scoring grids ==
			=== general ===
	= grids =
	== general ~~for all grids~~ ==
	* makebox.log		* makebox.log
	* box		* box

			=== ChemGrid (VDW) grids ===
	== ~~Files for~~ ChemGrid (VDW) grids ==
	* OUTCHEM		* OUTCHEM
	* vdw.bmp		* vdw.bmp
Line 38:		Line 46:
	* rec.crg.pdb.dms		* rec.crg.pdb.dms

	== Electrostatics ~~with~~ qnifft ==		=== Electrostatics (qnifft) ===
	* qnifft.electrostatics.phi		* qnifft.electrostatics.phi
	* qnifft.eps		* qnifft.eps
Line 48:		Line 56:


	== ~~Files for~~ ligand desolvation grids ==		=== ligand desolvation grids ===
	* ligand.desolv.heavy		* ligand.desolv.heavy
	* ligand.desolv.hydrogen		* ligand.desolv.hydrogen


	= receptor model =		== receptor model ==
	* lowdielectric.sph.pdb		* lowdielectric.sph.pdb


	= unsorted =		== unsorted ==
	* lowdielectric.sph.pdb.log		* lowdielectric.sph.pdb.log
	* filter.log		* filter.log

Frodo at 17:57, 23 February 2014

2014-02-23T17:57:31Z

← Older revision		Revision as of 17:57, 23 February 2014
Line 2:		Line 2:
	These are also documented with each associated program, but since [[Blastermaster]] is the widely used interface for docking, they are collected and organized here.		These are also documented with each associated program, but since [[Blastermaster]] is the widely used interface for docking, they are collected and organized here.

			{{TOCright}}

	= Files for spheres (hot spots) =		= Files for spheres (hot spots) =
Line 80:		Line 80:
	* qnifft.atm		* qnifft.atm
	* rec.site		* rec.site


			Blastermaster first appeared in [[DOCK 3.7]].

Frodo: Created page with "Meaning of the files created by Blastermaster. These are also documented with each associated program, but since Blastermaster is the widely used interface for docking, t..."

2014-02-23T17:56:18Z

Created page with "Meaning of the files created by Blastermaster. These are also documented with each associated program, but since Blastermaster is the widely used interface for docking, t..."

New page

Meaning of the files created by Blastermaster.
These are also documented with each associated program, but since [[Blastermaster]] is the widely used interface for docking, they are collected and organized here.

= Files for spheres (hot spots) =
* matching_spheres.log
* matching_spheres.sph
* all_spheres.sph
* rec.site.dms
* OUTSPH
* dms.log
* vdw.siz

= receptor protonation =
* addh.log
* reduce_wwPDB_het_dict.txt

= grids =
== general for all grids ==
* makebox.log
* box

== Files for ChemGrid (VDW) grids ==
* OUTCHEM
* vdw.bmp
* vdw.esp
* vdw.log
* OUTPARM
* INCHEM
* PDBPARM
* rec.crg.pdb
* vdw.parms.amb.mindock
* rec.crg.pdb.dms

== Electrostatics with qnifft ==
* qnifft.electrostatics.phi
* qnifft.eps
* qnifft.log
* qnifft.parm
* qnifft_sas.usr
* amb.crg.oxt
* trim.electrostatics.phi

== Files for ligand desolvation grids ==
* ligand.desolv.heavy
* ligand.desolv.hydrogen

= receptor model =
* lowdielectric.sph.pdb

= unsorted =
* lowdielectric.sph.pdb.log
* filter.log
* radii
* heavy
* hydrogen
* rec.crg.pdb.fullh
* vdw.vdw
* INSPH
* post-most.occ.rec.pdb
* rec.crg.pdb.polarH
* xtal-lig.match.sph
* pre-most.occ.rec.pdb
* receptor.crg.lowdielectric.pdb
* xtal-lig.pdb
* pre-rename.xtal-lig.pdb
* rec.ms
* lowdielectric.sph
* prot.table.ambcrg.ambH
* rec.pdb
* lowdielectric.spheres.log
* qnifft.atm
* rec.site

[[Category:Manual]]
[[Category:DOCK 3.7]]
[[Category:Internal]]