Rosetta

Rosetta is a software suite that 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.

 

Availability and Restrictions

Versions

The Rosetta suite is available on Owens and Pitzer. The versions currently available at OSC are:

 

Version Owens Pitzer
3.10 X X
3.12 X* X*
* Current default version

You can use  module spider rosetta to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users 

Rosetta is available to academic OSC users. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Rosetta, Non-Commercial

Usage

Usage on Owens and Pitzer

To set up your environment for rosetta load one of its module files:

​​module load rosetta/3.12

Here is an example batch script that uses Rosetta Abinitio Relax application:

#!/bin/bash
#SBATCH --job-name="rosetta_abinitio_relax_job"
#SBATCH --ntasks=1
#SBATCH --time=0:10:0
#SBATCH --account=PAS1234

qstat -f $SLURM_JOB_ID
export

module reset
module load rosetta/3.12
module list

pbsdcp -rp $ROSETTA3/demos/tutorials/denovo_structure_prediction/* $TMPDIR
cd $TMPDIR
AbinitioRelax.linuxiccrelease @input_files/options

ls -l
pbsdcp --gather --recursive --preserve '*' $SLURM_SUBMIT_DIR

Here is an example batch script that uses Rosetta MPI Docking script:

#!/bin/bash
#SBATCH --job-name="rosetta_scripts_mpi_docking_job"
#SBATCH --nodes=2
#SBATCH --time=0:10:0
#SBATCH --account=PAS1234 

qstat -f $SLURM_JOB_ID
export
 
module reset
module load rosetta/3.12
module list

pbsdcp ~support/share/reframe/source/rosetta/6shs_PIB.pdb $TMPDIR
pbsdcp ~support/share/reframe/source/rosetta/pib-abeta.xml $TMPDIR
pbsdcp ~support/share/reframe/source/rosetta/pib.params $TMPDIR

cd $TMPDIR
srun rosetta_scripts.mpi -s 6shs_PIB.pdb -nstruct 100 -extra_res_fa pib.params -parser:protocol pib-abeta.xml -add_orbitals True -out:prefix t_ -out:pdb True

pbsdcp --gather --recursive --preserve '*' $SLURM_SUBMIT_DIR

Further Reading

 
Supercomputer: 
Service: