Difference between revisions of "Blastermaster files"

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(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...")
 
 
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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}}
  
= Files for spheres (hot spots) =  
+
= dockfiles directory =
 +
 
 +
== posing ==
 +
* matching_spheres.sph - spheres (hotspots)
 +
* vdw.bmp - bump map to rapidly eliminate unproductive poses
 +
 
 +
== scoring ==
 +
* 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 directory =
 +
== spheres (hotspots) ==  
 
* matching_spheres.log
 
* matching_spheres.log
 
* matching_spheres.sph  
 
* matching_spheres.sph  
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* vdw.siz
 
* vdw.siz
  
 
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== protonation ==  
= receptor protonation =  
 
 
* addh.log
 
* addh.log
 
* reduce_wwPDB_het_dict.txt
 
* reduce_wwPDB_het_dict.txt
  
 
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== scoring grids ==  
 
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=== general ===
= grids =  
 
== general for all grids ==
 
 
* makebox.log
 
* makebox.log
 
* box
 
* box
  
 
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=== VdW (ChemGrid) scoring grids ===  
== Files for ChemGrid (VDW) grids ==  
 
 
* OUTCHEM
 
* OUTCHEM
 
* vdw.bmp
 
* vdw.bmp
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* rec.crg.pdb.dms
 
* rec.crg.pdb.dms
  
== Electrostatics with qnifft ==  
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=== Electrostatics (qnifft) scoring grids ===  
 
* qnifft.electrostatics.phi
 
* qnifft.electrostatics.phi
 
* qnifft.eps
 
* qnifft.eps
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* trim.electrostatics.phi
 
* trim.electrostatics.phi
  
 
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=== ligand desolvation grids ===  
== Files for ligand desolvation grids ==  
 
 
* ligand.desolv.heavy
 
* ligand.desolv.heavy
 
* ligand.desolv.hydrogen
 
* ligand.desolv.hydrogen
  
  
= receptor model =  
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== to be sorted ==  
* lowdielectric.sph.pdb
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* lowdielectric.sph.pdb                
 
 
 
= unsorted =                 
 
 
* lowdielectric.sph.pdb.log
 
* lowdielectric.sph.pdb.log
 
* filter.log
 
* filter.log
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* rec.site
 
* rec.site
  
 +
 +
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]]

Latest revision as of 15:10, 25 March 2014

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.

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.

dockfiles directory

posing

  • matching_spheres.sph - spheres (hotspots)
  • vdw.bmp - bump map to rapidly eliminate unproductive poses

scoring

  • 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 directory

spheres (hotspots)

  • matching_spheres.log
  • matching_spheres.sph
  • all_spheres.sph
  • rec.site.dms
  • OUTSPH
  • dms.log
  • vdw.siz

protonation

  • addh.log
  • reduce_wwPDB_het_dict.txt

scoring grids

general

  • makebox.log
  • box

VdW (ChemGrid) scoring grids

  • OUTCHEM
  • vdw.bmp
  • vdw.esp
  • vdw.log
  • OUTPARM
  • INCHEM
  • PDBPARM
  • rec.crg.pdb
  • vdw.parms.amb.mindock
  • rec.crg.pdb.dms

Electrostatics (qnifft) scoring grids

  • qnifft.electrostatics.phi
  • qnifft.eps
  • qnifft.log
  • qnifft.parm
  • qnifft_sas.usr
  • amb.crg.oxt
  • trim.electrostatics.phi

ligand desolvation grids

  • ligand.desolv.heavy
  • ligand.desolv.hydrogen


to be sorted

  • lowdielectric.sph.pdb
  • 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


Blastermaster first appeared in DOCK 3.7. Return to Blastermaster.