Blastermaster files: Difference between revisions
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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}} | ||
= | = 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 == | |||
= | |||
* addh.log | * addh.log | ||
* reduce_wwPDB_het_dict.txt | * reduce_wwPDB_het_dict.txt | ||
== scoring grids == | |||
=== general === | |||
= grids = | |||
== general | |||
* makebox.log | * makebox.log | ||
* box | * box | ||
=== ChemGrid (VDW) grids === | |||
== | |||
* OUTCHEM | * OUTCHEM | ||
* vdw.bmp | * vdw.bmp | ||
| Line 38: | Line 46: | ||
* rec.crg.pdb.dms | * rec.crg.pdb.dms | ||
== Electrostatics | === Electrostatics (qnifft) === | ||
* qnifft.electrostatics.phi | * qnifft.electrostatics.phi | ||
* qnifft.eps | * qnifft.eps | ||
| Line 48: | Line 56: | ||
== | === 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.