Blastermaster files

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.