GOLD

GOLD is a docking program for predicting how flexible molecules will bind to proteins. GOLD uses a genetic algorithm methodology for protein-ligand docking and allows full ligand and partial protein flexibility.

Available

  • Puhti: 2020
  • DiscoveryStudio2019 server
  • Download and install locally

License

License cover academic usage at universities and non-profit research institutes. See our CSD page for details.

Usage

GOLD is part of the Cambridge Crystallographic Database System. See our CSD page for installation and activation.

GOLD can be used either from the command line or via a graphical user interface (GUI) called Hermes. The best way to run a GUI remotely on Puhti is to use the [NoMachine]. To set up the GOLD interactive environment:

module load ccdc

This will load the latest version of CSD and GOLD. The easiest way to run interactive jobs is to log Puhti via NoMachine, start an interactive session, finally GOLD.

module load ccdc
srun --ntasks=1 --time=00:10:00 --mem=1G --pty \
  --account=<project> --partition=small --mail-type=BEGIN \
  --mail-user=<your email address> bash  # and wait for resources to be granted
gold

We are currently developing a command and partition to provide interative resources more easily.

Longer (non-interactive) jobs are best run as batch jobs:

#!/bin/bash -l
#SBATCH --partition=small
#SBATCH --ntasks=1
#SBATCH --account=<project>
#SBATCH --time=0:30:00    # time as hh:mm:ss

module load ccdc

gold_auto gold.conf

Note

If you want to run GOLD in parallel, please contact us

Usage via Discovery Studio

GOLD is available in the DiscoveryStudio 2019 server at CSC.

More information