Ucsfdock: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 30: | Line 30: | ||
If your current working directory contains any of the following files | If your current working directory contains any of the following files | ||
* rec.pdb | * ''rec.pdb'' | ||
* xtal-lig.pdb | * ''xtal-lig.pdb'' | ||
* rec.crg.pdb | * ''rec.crg.pdb'' | ||
* reduce_wwPDB_het_dict.txt | * ''reduce_wwPDB_het_dict.txt'' | ||
* filt.params | * ''filt.params'' | ||
* radii | * ''radii'' | ||
* amb.crg.oxt | * ''amb.crg.oxt'' | ||
* vdw.siz | * ''vdw.siz'' | ||
* delphi.def | * ''delphi.def'' | ||
* vdw.parms.amb.mindock | * ''vdw.parms.amb.mindock'' | ||
* prot.table.ambcrg.ambH | * ''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 | then they will be automatically copied into the working directory within the generated blastermaster job directory. If you would like to use | ||
Revision as of 08:41, 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.
Programs:
- 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