LigandMPNN

Inputs

• Place structure inputs (PDB plus ligand files) under /inputs.
• Batch mode: -I=<dir> (e.g. -I=/inputs) processes all input files in a folder.
• Results and designed sequences are written to /outputs.

Example arguments

Defaults that mirror the New Job prefill:

--model_type=protein_mpnn
-I=/inputs
--out_folder=/outputs
--temperature=0.05
--checkpoint_protein_mpnn=/ref/model_params/proteinmpnn_v_48_020.pt

Tweak --temperature or swap checkpoints if you have custom weights.

Submit

Launch via New Job -> LigandMPNN.

Output notes

• LigandMPNN produces a multi-FASTA output. The first record is the input sequence when available.
• For backbone-only inputs, the “input sequence” is often all glycine (not useful for many downstream tools).
• The designed (generated) sequence is often the second record and is typically what you want to extract/use downstream.