Rosetta

Description

From: The Rosetta website: The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

Version

  • 3.5

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Rosetta requires the following module file to run:

  • apps/rosetta/3.5

Running Rosetta on CIRCE/SC

The Rosetta user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting a Job

  • The script below (for testing, call it “rosetta-test.sh”) can be copied into your job directory (the folder with your input files and database files) and modified so that you can submit batch processes to the queue.


#!/bin/bash
#
#SBATCH --job-name=Rosetta-Test
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --output=output.%j.Rosetta-Test
#SBATCH --time=01:00:00

#### SLURM 2 node, 4 cores per node Rosetta test for 1 hour

module purge
module load apps/rosetta/3.5

mpirun rosetta_scripts.mpi.linuxgccrelease -database ${ROSETTA_DB} \ 
         @rosetta.options &>> rosetta.log

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./rosetta-test.sh
  • You can view the status of your job with the “squeue -u <username>” command
    • NOTE: Rosetta has many different executables and options for the command line. It is important that you read and understand the Rosetta User Guide in order to use the software effectively and run jobs on the cluster. The best place to begin is the Getting Started with Rosetta guide.

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Rosetta to the IT Help Desk: rc-help@usf.edu