Blastermaster files: Difference between revisions
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{{TOCright}} | {{TOCright}} | ||
= dockfiles = | = dockfiles directory = | ||
* matching_spheres.sph | == posing == | ||
* vdw.bmp | * matching_spheres.sph - spheres (hotspots) | ||
* | * 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 directory = | ||
== spheres (hotspots) == | == spheres (hotspots) == | ||
* matching_spheres.log | * matching_spheres.log | ||
| Line 34: | Line 38: | ||
* box | * box | ||
=== ChemGrid | === VdW (ChemGrid) scoring grids === | ||
* OUTCHEM | * OUTCHEM | ||
* vdw.bmp | * vdw.bmp | ||
| Line 46: | 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 54: | Line 58: | ||
* amb.crg.oxt | * amb.crg.oxt | ||
* trim.electrostatics.phi | * trim.electrostatics.phi | ||
=== ligand desolvation grids === | === ligand desolvation grids === | ||
| Line 61: | Line 64: | ||
== | == to be sorted == | ||
* lowdielectric.sph.pdb | * lowdielectric.sph.pdb | ||
* lowdielectric.sph.pdb.log | * lowdielectric.sph.pdb.log | ||
* filter.log | * filter.log | ||
| 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]] | ||
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.