RFdiffusion2 on the cluster

RFdiffusion2 is a protein generation and design tool from the Baker laboratory for tasks including backbone design, binding-site design, and small-molecule binder design. The CHESS application accepts JSON inputs and schedules resources automatically.

Prepare inputs

Sign in to CHESS:

Suggested JSON and output paths (用户名 means your username):

/hpcfs/fhome/用户名/rfdiffusion2/input/open_source_demo.json

/hpcfs/fhome/用户名/rfdiffusion2/output/

Example JSON fragment; adapt the task, input PDB, ligands, and contig settings:

{
  "active_site_indexed_atomic": "inference.input_pdb=mcsa_41/M0584_1ldm.pdb inference.ligand='NAD,OXM' contigmap.contigs=['46,A106-106,59,A166-166,2,A169-169,23,A193-193,46'] inference.contig_as_guidepost=False",
  "small_molecule_binder_rasa_buried": "inference.conditions.relative_sasa_v2.active=True inference.conditions.relative_sasa_v2.rasa=0 contigmap.contigs=['150'] inference.input_pdb=trimmed_ec2_M0151_NO_ORI_zero_com0.pdb contigmap.length=150-150 inference.ligand=PH2"
}

Submit through CHESS

Find RFdiffusion2 in Application Center (应用中心) and add it to the desktop:

Open it, select the JSON input, and set the output directory:

Use a valid JSON file that matches the application requirements. Update PDB, ligand, and output references for your task. Ensure write permission and use separate outputs for different batches or templates.

View status and progress in Job Management (作业管理):

Open job details for standard output, errors, and logs:

Demonstration:

Results and troubleshooting

The output directory may contain generated structures, logs, scoring/filtering files, and per-input or per-template subdirectories. Inspect logs, JSON parameters, paths, and permissions if results are absent.

GPU jobs can wait when resources are busy. Input paths must identify readable files on the cluster. Output directories must be writable; shared access requires administrator configuration. Start with a platform example, then adapt parameters one at a time to your structure, ligands, and design goals.