AlphaFold 2

/fs00/software/alphafold/2.3.2/AlphaFold-v2.3.2.sif

#BSUB -J alphafold
#BSUB -q gpu
#BSUB -n 16
#BSUB -gpu num=1

export OMP_NUM_THREADS="$LSB_DJOB_NUMPROC"
export MKL_NUM_THREADS="$LSB_DJOB_NUMPROC"

ALPHAFOLD_DATADIR=/bbfs/data/alphafold
ALPHAFOLD_IMAGE=AlphaFold-v2.3.2.sif

ALPHAFOLD_APP=/app/alphafold

RUN_ALPHAFOLD="apptainer run --bind ${ALPHAFOLD_DATADIR}:${ALPHAFOLD_APP}/download \
                            --nv ${ALPHAFOLD_IMAGE}"

${RUN_ALPHAFOLD} python ${ALPHAFOLD_APP}/run_alphafold.py --use_gpu_relax \
    --data_dir=${ALPHAFOLD_APP}/download \
    --uniref90_database_path=${ALPHAFOLD_APP}/download/uniref90/uniref90.fasta \
    --mgnify_database_path=${ALPHAFOLD_APP}/download/mgnify/mgy_clusters_2022_05.fa \
    --bfd_database_path=${ALPHAFOLD_APP}/download/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
    --pdb70_database_path=${ALPHAFOLD_APP}/download/pdb70/pdb70 \
    --uniref30_database_path=${ALPHAFOLD_APP}/download/uniref30/UniRef30_2021_03 \
    --template_mmcif_dir=${ALPHAFOLD_APP}/download/pdb_mmcif/mmcif_files \
    --obsolete_pdbs_path=${ALPHAFOLD_APP}/download/pdb_mmcif/obsolete.dat \
    --model_preset=monomer \
    --max_template_date=2022-10-1 \
    --db_preset=full_dbs \
    --output_dir=output \
    --fasta_paths=input/input.fasta