Installing SBGrid Software
Using the SBGrid Environment
Support for Site Administrators
Hardware Support Notes
Getting Help
Support for Developers
In order to run AlphaFold3 with SBGrid you must: 1. Obtain the AF3 models 2. Download the AF3 databases
SBGrid cannot distribute these. You must apply through this form:
https://forms.gle/svvpY4u2jsHEwWYS6
The link for the form is also given in the git repository
You will receive a link to download the models as a zstd compressed file. Uncompress this file to produce af3.bin. Place this file in a directory of your choice. You must supply this directory as an argument to the run_alphafold.py script.
The databases for AlphaFold3 (AF3) must be downloaded.
AlphaFold provides a script for downloading these in the github repo:
https://github.com/google-deepmind/alphafold3/blob/main/fetch_databases.sh
The version of AF3 curated in SBGrid uses the tar file version of the mmcif files in pdb_2022_09_28_mmcif_files.tar.
Since then AF3 has changed to use the uncompressed files in the mmcif tar file. The download script will untar the file.
The resulting layout should look like this:
/programs//local/alphafold-3.0.0/databases/
├── bfd-first_non_consensus_sequences.fasta
├── compressed
│ ├── bfd-first_non_consensus_sequences.fasta.zst
│ ├── mgy_clusters_2022_05.fa.zst
│ ├── nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta.zst
│ ├── pdb_2022_09_28_mmcif_files.tar.zst
│ ├── pdb_seqres_2022_09_28.fasta.zst
│ ├── rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta.zst
│ ├── rnacentral_active_seq_id_90_cov_80_linclust.fasta.zst
│ ├── uniprot_all_2021_04.fa.zst
│ └── uniref90_2022_05.fa.zst
├── mgy_clusters_2022_05.fa
├── nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta
├── pdb_2022_09_28_mmcif_files.tar
├── pdb_seqres_2022_09_28.fasta
├── rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta
├── rnacentral_active_seq_id_90_cov_80_linclust.fasta
├── uniprot_all_2021_04.fa
└── uniref90_2022_05.fa