AlphaFold 3¶

We provide AlphaFold v3.0.4 on the HPC as Singularity containers located in /local/cqls/singularity/images/. Both x86 and ARM containers are provided. By using these containers you acknowledge the AlphaFold 3 model parameters terms of service.

The command to run the x86 container is:

singularity run --nv \
  --bind /local/cqls/db,/scratch \
  /local/cqls/singularity/images/alphafold_v3.0.4_x86.sif \
  --model_dir=/local/cqls/db/alphafold3_params \
  --db_dir=/local/cqls/db/alphafold3 \
  --json_path=input/fold_input.json \
  --output_dir=output

This command assumes that in your working directory you have an input file fold_input.json that is in the input folder and the output will be sent to the output folder.

Adjust these variables to your preference. Change alphafold_v3.0.4_x86.sif to alphafold_v3.0.4_arm.sif to run the ARM container.

To see the full or short help menus, run singularity run --nv /local/cqls/singularity/images/alphafold_v3.0.4_x86.sif with the --helpfull or --helpshort flags.