Table of Contents

Warning

Do not share model weights, they are protected by a license!

Starting a Job

1. Create a working directory with two subfolders: input and output

2. Place your JSON input file into the input folder (input format documentation). Example: 

{
  "name": "2PV7",
  "sequences": [
    {
     "protein": {
       "id": ["A", "B"],
       "sequence": "GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3", 
  "version": 1
}

3. Create a Slurm job from Templates

4. Adjust the job script (for more details see Slurm Guide)

5. Start the Job

Prediction Size Estimate (approximate)

Molecule type What 1 token represents 24 GB VRAM estimate 48 GB VRAM estimate
Protein 1 amino acid residue ~2,800 residues ~4,000 residues
DNA / RNA 1 nucleotide ~2,800 nt ~4,000 nt
Ligand 1 atom ~2,800 atoms ~4,000 atoms
Ion / cofactor 1 atom / entity ~2,800 entities ~4,000 entities
Mixed complex Sum of all tokens across chains + ligands ~2,800 tokens total ~4,000 tokens total