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.
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* |
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.
Rosetta is available to academic OSC users. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.
Rosetta, Non-Commercial
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
scontrol show job $SLURM_JOB_ID
export
module reset
module load rosetta/3.12
module list
echo $TMPDIR
cd $TMPDIR
mkdir input_files
sbcast -p $ROSETTA3/demos/tutorials/denovo_structure_prediction/Denovo_structure_prediction.md $TMPDIR/Denovo_structure_prediction.md
sbcast -p $ROSETTA3/demos/tutorials/denovo_structure_prediction/folding_funnels.png $TMPDIR/folding_funnels.png
cd $ROSETTA3/demos/tutorials/denovo_structure_prediction/input_files/
for FILE in *
do
sbcast -p $FILE $TMPDIR/input_files/$FILE
done
cd $TMPDIR
AbinitioRelax.linuxiccrelease @input_files/options
ls -l
sgather -pr $TMPDIR ${SLURM_SUBMIT_DIR}/sgather
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
scontrol show job $SLURM_JOB_ID
export
module reset
module load rosetta/3.12
module list
sbcast -p ~support/share/reframe/source/rosetta/6shs_PIB.pdb $TMPDIR/6shs_PIB.pdb
sbcast -p ~support/share/reframe/source/rosetta/pib-abeta.xml $TMPDIR/pib-abeta.xml
sbcast -p ~support/share/reframe/source/rosetta/pib.params $TMPDIR/pib.params
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
sgather -pr $TMPDIR ${SLURM_SUBMIT_DIR}/sgather