parallel_gold

Run GOLD in parallel by splitting the sdf-file containing the ligands for docking into smaller sdf-files and run separate docking jobs.

Install

Clone this repository

Open a new terminal and clone this repository.

cd ~
git clone https://github.com/schallerdavid/parallel_gold.git

Dependencies

This tool requires Ṕython>=3.5 and a working GOLD installation. It was only tested on linux. The system needs to be able to handle the alias "gold_auto".

Create alias for your bash or c shell

echo 'alias parallel_gold="python3 ~/parallel_gold/parallel_gold.py"' >> ~/.bashrc

or

echo 'alias parallel_gold "python3 ~/parallel_gold/parallel_gold.py"' >> ~/.cshrc

Run parallel_gold

Generate a gold.conf-file for your system. The docking poses need to be saved in a single output file (specified as concatenated_output in gold conf-file).

Open a terminal, change to project directory and run parallel_gold.

cd docking_directory
parallel_gold -g gold.conf -p 6

Can be also used to submit jobs via slurm.

parallel_gold -g gold.conf -s cn-cpu -p 28

Copyright

Copyright (c) 2020, David Schaller