Difference between revisions of "Blastermaster files"

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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 =  

Revision as of 15:08, 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

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

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

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 (qnifft)

  • 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


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


Blastermaster first appeared in DOCK 3.7.