CB DOCK 3.8 tutorial

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

• WIP