Difference between revisions of "Blastermaster files"

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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  
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* 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
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* rec.crg.pdb.dms
 
* rec.crg.pdb.dms
  
== Electrostatics with qnifft ==  
+
=== Electrostatics (qnifft) ===  
 
* qnifft.electrostatics.phi
 
* qnifft.electrostatics.phi
 
* qnifft.eps
 
* qnifft.eps
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== 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

Revision as of 15:03, 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

  • 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.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.