Rosetta

The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.

Usage

#!/bin/bash
#SBATCH -J testRosetta # job name
#SBATCH -N 1 # total number of nodes
#SBATCH --cpus-per-task=4
#SBATCH --output=testRosetta-%j.out #output file (%j expands to jobID)
#SBATCH --error=testRosetta-%j.err #error file (%j expands to jobID)
#SBATCH -p thin # partition

module load autotools
module load prun/2.2
module load gnu12/12.2.0
module load hwloc/2.7.0
module load ucx/1.11.2
module load libfabric/1.13.0
module load ohpc
module load openmpi4/4.1.4
module load rosetta/3.7.1

export ROSETTA3=/opt/ohpc/pub/apps/rosetta/rosetta.binary.linux.release-371/main/source/
export ROSETTA3_DB=/opt/ohpc/pub/apps/rosetta/rosetta.binary.linux.release-371/main/database/
export PATH=/opt/ohpc/pub/apps/rosetta/scons/:$ROSETTA3/bin:$PATH

mpirun $ROSETTA3/bin/rna_denovo.static.linuxgccrelease @flags_run

flags_run file

    -in:ignore_unrecognized_res
    -fasta xyz.fasta
    -secstruct_file xyz.secstruct
    -nstruct 1000
    -out:file:silent xyz.out
    -cycles 1000
    -minimize_rna true
    -allow_complex_loop_graph
    -run:ignore_zero_occupancy false
    -bps_moves true
    -use_legacy_job_distributor true
    -score:weights rna_res_level_energy4.wts
    -restore_talaris_behavior

More info :

• https://rosettacommons.org/