CB DOCK 3.8 tutorial: Difference between revisions

From DISI
Jump to navigation Jump to search
(Creation)
 
 
(4 intermediate revisions by the same user not shown)
Line 25: Line 25:
* Protein preparation
* Protein preparation
* WIP
* WIP
==  Pydock3 dockopt ==
* https://wiki.docking.org/index.php/Dockopt_(pydock3_script)
0) Don't forget to be on gimel5
1) Create actives.tgz and decoys.tgz files :
* Create "actives" and "decoys" folders, and put every db2 files you have inside
* Compression using :
<nowiki>tar -cvzf actives.tgz $PWD/actives/*
tar -cvzf decoys.tgz $PWD/decoys/*</nowiki>
2) Copy rec.pdb and xtal-lig.pdb in the main folder
3) Initialization of dockopt :
<nowiki>pydock3 dockopt - init JobName</nowiki>
4) Define environment variables and run dockopt :
<nowiki>cd JobName/
export SBATCH_EXEC=/usr/bin/sbatch
export SQUEUE_EXEC=/usr/bin/squeue
export TMPDIR=/scratch
pydock3 dockopt - run slurm</nowiki>


==  DOCK 3.8 docking ==
==  DOCK 3.8 docking ==
Line 47: Line 71:
* In gimel5, --use-slurm=true is mandatory
* In gimel5, --use-slurm=true is mandatory
  <nowiki>
  <nowiki>
bash /nfs/home/cbedart/exk/DOCK/ucsfdock/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true</nowiki>
bash $DOCKBASE/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true</nowiki>


==  DOCK 3.8 analysis ==
==  DOCK 3.8 analysis ==
* WIP
 
 
=== top_poses.py ===
 
1) Load a specific python environment :
* (why is it different from the version used to run pydock3 ?)
<nowiki>source /nfs/soft/python/versions/python-3.8-install/bin/env.sh</nowiki>
 
2) Main commands :
* https://wiki.docking.org/index.php/Docking_Analysis_in_DOCK3.8#Note_on_Parallel_Processing
* 2022/12/13 : instructions doesn't seem to work, only the script and the main path
<nowiki>python3 $DOCKBASE/analysis/top_poses.py output/</nowiki>

Latest revision as of 18:37, 15 December 2022

Things to remember

  • Be in gimel5 : ssh gimel5

DOCK 3.8 installation

1) Download pydock3 : 

git clone https://github.com/docking-org/pydock3

2) Download DOCK engine : 

cd ./pydock3/
git clone https://github.com/docking-org/DOCK.git

3) Add in your ~/.profile file :

  • python 3.8.5 environment (gimel5)
  • DOCKEXEC & DOCKBASE environment variables
source /nfs/soft/ian/python3.8.5.sh
export DOCKEXEC=''>PATH<''/pydock3/DOCK/ucsfdock/docking/DOCK/dock64
export DOCKBASE=''>PATH<''/pydock3/DOCK/ucsfdock
  • Do not forget to source ~/.profile in case you plan to use DOCK & pydock3 immediately

Pydock3 blastermaster

  • Protein preparation
  • WIP


Pydock3 dockopt

0) Don't forget to be on gimel5

1) Create actives.tgz and decoys.tgz files :

  • Create "actives" and "decoys" folders, and put every db2 files you have inside
  • Compression using :
tar -cvzf actives.tgz $PWD/actives/*
tar -cvzf decoys.tgz $PWD/decoys/*

2) Copy rec.pdb and xtal-lig.pdb in the main folder

3) Initialization of dockopt : 

pydock3 dockopt - init JobName

4) Define environment variables and run dockopt : 

cd JobName/
export SBATCH_EXEC=/usr/bin/sbatch
export SQUEUE_EXEC=/usr/bin/squeue
export TMPDIR=/scratch
pydock3 dockopt - run slurm

DOCK 3.8 docking

1) Create your run directory and copy dockfiles from blastermaster :

2) Import ligands, and create ligand index file :

  • Important notice : The index file must be filled with absolute paths
find $PWD -type f -name '*.db2*' > sdi.in

3) Create an init.sh file to initialize the main environment variables that will be used during docking : 

export INPUT_SOURCE=$PWD/sdi.in
export EXPORT_DEST=$PWD/output
export DOCKFILES=$PWD/dockfiles

4) Load your init.sh file : 

source ./init.sh

5) Run docking :

  • In case of db2.gz files from TLDR, use --use-db2=true --use-db2-tgz=false options
  • In gimel5, --use-slurm=true is mandatory
bash $DOCKBASE/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true

DOCK 3.8 analysis

top_poses.py

1) Load a specific python environment :

  • (why is it different from the version used to run pydock3 ?)
source /nfs/soft/python/versions/python-3.8-install/bin/env.sh

2) Main commands : 

python3 $DOCKBASE/analysis/top_poses.py output/
Retrieved from "http://wiki.docking.org/index.php?title=CB_DOCK_3.8_tutorial&oldid=15047"