Ucsfdock: Difference between revisions

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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:
1. ''working'': blaster files, sub-directories for individual subroutines
2. ''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

Latest revision as of 22:56, 24 May 2024

See pydock3.