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: 2022
- Download and install locally
License
License covers academic usage at universities and non-profit research institutes. See our CSD page for details.
Usage
GOLD is a part of the Cambridge Crystallographic Database System. See our CSD page for installation and activation instructions.
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 Puhti web interface desktop. To set up
the GOLD interactive environment, open a Host Terminal and run:
module load ccdc/2022
This will load the latest version of CSD and GOLD. To run GOLD you can either enter hermes and navigate to the GOLD tab, or alternatively run gold which opens the GOLD wizard of Hermes directly. Note that the GUI performance can be somewhat slow as the Puhti web interface does not provide accelerated graphics for Hermes.
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 CSC Service Desk.