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GOLD

GOLD

Description

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

Version on CSC's Servers


Usage

License

GOLD is part of the Cambridge Crystallographic Database System. See our CSD page for licensing information.

GOLD can be used either from the command line or via a graphical user interface (GUI). The best way to run a GUI remotely is to use the NoMachine Remote Desktop service available for CSC users. To set up the GOLD interactive environment:

module load ccdc

This will load the latest version of GOLD. The easiest way to run interactive jobs is to log in to taito-shell and start gold with the command gold. If you want dedicated interactive resources, you start interactive session on a compute node, type:

salloc -p serial -n 1 -t 02:00:00 srun --x11=first xterm

Launch the gold command in the xterm. Longer jobs are best run as batch jobs, see below.
 

NOTE: Gold license now covers unlimited simultaneous jobs.

The PVM daemon must be running before parallel GOLD dockings can be started. After docking, the PVM daemon should be stopped and all its generated files removed. In principle it is possible to run several docking jobs simultaneously, but if two PVM jobs run on the same node, problems might arise

This example job script is for a serial job. Submit it on Taito with:

sbatch job-gold2019-taitoser.job

This example job script would start a job on 4 CPU's.

sbatch job-gold2019-taitopar.job

Usage via Discovery Studio or Maestro

GOLD is available in  the Discovery Studio 2018 server and Maestro at CSC. This GOLD installation can be used with locally installed Discovery Studio molecular modeling program, but to use with locally installed Maestro, you need to install GOLD locally also.

 


Discipline

Biosciences
Chemistry

References


Support


Manual