download_dir=/data/alphafold2 
python3 run_alphafold.py \
 --fasta_paths=multimer.fasta \
 --output_dir=./ \
 --num_multimer_predictions_per_model=1 \
 --use_precomputed_msas=false \
 --data_dir=$download_dir  \
 --model_names="model_1_multimer_v3" \
 --uniref90_database_path=$download_dir/uniref90/uniref90.fasta \
 --mgnify_database_path=$download_dir/mgnify/mgy_clusters_2022_05.fa \
 --bfd_database_path=$download_dir/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
 --uniref30_database_path=$download_dir/uniref30/UniRef30_2021_03 \
 --uniprot_database_path=$download_dir/uniprot/uniprot.fasta \
 --pdb_seqres_database_path=$download_dir/pdb_seqres/pdb_seqres.txt \
 --template_mmcif_dir=$download_dir/pdb_mmcif/mmcif_files \
 --obsolete_pdbs_path=$download_dir/pdb_mmcif/obsolete.dat \
 --max_template_date=2020-05-14 \
 --model_preset=multimer \
 --db_preset=full_dbs \
 --models_to_relax=best \
 --use_gpu_relax=false 

