CB DOCK 3.8 tutorial
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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
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 :
- 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
python3 $DOCKBASE/analysis/top_poses.py output/