version 2


Please refer to the following command for usage, which requires activating the conda environment.

module load conda

module load af2/2.3.2

cd /spshared/apps/alphafold

python3 /spshared/apps/alphafold/docker/run_docker.py --fasta_paths=test.fasta --max_template_date=2020-05-14 --data_dir=/data/af2_db --output_dir=/XX/XX/XX


Parameter Explanation

  • --fasta_paths, The path of the fasta file, please use an absolute path and make sure fasta exists.
  • --data_dir, The database path of alphafold is usually stored in /data/af2_db. Please modify it according to the actual situation.
  • --output_dir, The storage path of the calculation results must be readable and writable.



version 3


alphafold3 requires model parameters, please apply for it in the following link.

https://docs.google.com/forms/d/e/1FAIpQLSfWZAgo1aYk0O4MuAXZj8xRQ8DafeFJnldNOnh_13qAx2ceZw/viewform


Please execute the following command to run alphafold3


/spshared/apps/alphafold3/

singularity exec \

     --nv \

     --bind $HOME/af_input:/root/af_input \

     --bind $HOME/af_output:/root/af_output \

     --bind <MODEL_PARAMETERS_DIR>:/root/models \

     --bind <DB_DIR>:/root/public_databases \

     alphafold3.sif \

     python run_alphafold.py \

     --json_path=/root/af_input/fold_input.json \

     --model_dir=/root/models \

     --db_dir=/root/public_databases \

     --output_dir=/root/af_output


Parameter Explanation

  • --bind $HOME/af_input, specifies the input path of the data;
  • --bind $HOME/af_output, specifies the output path of the data;
  • --bind <MODEL_PARAMETERS_DIR>, the path of the model parameters;
  • --bind <DATABASES_DIR>, the path of the database;
  • --json_path, specifies the path of the json file inside singularity;
  • --input_dir, specifies the path of the JSON file, and this parameter is used when there are multiple files. It is incompatible with --json_path.
  • /root, refers to the path inside the singularity container;