Ucsfdock: Difference between revisions
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blastermaster configure | blastermaster configure | ||
By default, the job directory is named 'blastermaster_job'. To specify the name, you can do | By default, the job directory is named 'blastermaster_job'. To specify the job directory name, you can do | ||
blastermaster configure <JOB_DIR_NAME> | blastermaster configure <JOB_DIR_NAME> | ||
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- prot.table.ambcrg.ambH | - prot.table.ambcrg.ambH | ||
then they will be copied into the working directory within the generated blastermaster job directory. | then they will be copied into the working directory within the generated blastermaster job directory. | ||
== dockamster == | == dockamster == | ||
# TODO | # TODO | ||
Revision as of 08:13, 28 July 2022
ucsfdock is a Python package wrapping the DOCK program that provides tools to help standardize and automate the computational methods employed in molecular docking.
Scripts: - 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
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 the job directory name, you can do
blastermaster configure <JOB_DIR_NAME>
If your current working directory contains any of the following files
- 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 copied into the working directory within the generated blastermaster job directory.
dockamster
- TODO