Ucsfdock: Difference between revisions

Latest revision as of 22:56, 24 May 2024

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-''ucsfdock'' is a Python package wrapping the [[DOCK|DOCK program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.
+See [[pydock3]].
-Programs:
+[[Category:Deprecated]]
-* blastermaster: given receptor and ligand, generate a specific docking configuration
-* dockmaster: evaluate many different docking configurations in parallel using a provided job scheduler (e.g. Slurm)
-= Installation =
-# TODO
-= Quickstart =
-== blastermaster ==
-=== blastermaster configure ===
-First you need to create the directory for your blastermaster job. To do so, simply type
- blastermaster configure
-By default, the job directory is named ''blastermaster_job''. To specify a different name, type
- blastermaster configure <JOB_DIR_NAME>
-The job directory contains two sub-directories:
-# ''working'': blaster files, sub-directories for individual subroutines
-# ''dockfiles'': DOCK parameter files & INDOCK file
-If your current working directory contains any of the following files
-* rec.pdb
-* xtal-lig.pdb
-* rec.crg.pdb
-* reduce_wwPDB_het_dict.txt
-* filt.params
-* radii
-* amb.crg.oxt
-* vdw.siz
-* delphi.def
-* vdw.parms.amb.mindock
-* prot.table.ambcrg.ambH
-then they will be automatically copied into the working directory within the generated blastermaster job directory. If you would like to use
-=== blastermaster run ===
-Now
-== dockamster ==
-# TODO