> ## Documentation Index
> Fetch the complete documentation index at: https://mintlify.com/google-deepmind/alphafold3/llms.txt
> Use this file to discover all available pages before exploring further.

# Known Issues

> Known issues and workarounds for AlphaFold 3

## Numerical Performance for CUDA Capability 7.x GPUs

<Warning>
  All CUDA Capability 7.x GPUs (e.g. V100) produce obviously bad output, with lots of clashing residues.
</Warning>

### Issue Description

When running AlphaFold 3 on CUDA Capability 7.x GPUs (such as the V100), the model produces poor quality predictions with:

* Lots of clashing residues
* Ranking scores of -99 or lower
* Generally unusable output

### Workaround

Set the `XLA_FLAGS` environment variable to include the following flag:

```bash theme={null}
export XLA_FLAGS="--xla_disable_hlo_passes=custom-kernel-fusion-rewriter"
```

When running with Docker, pass this environment variable:

```bash theme={null}
docker run -it \
    --env XLA_FLAGS="--xla_disable_hlo_passes=custom-kernel-fusion-rewriter" \
    --volume $HOME/af_input:/root/af_input \
    --volume $HOME/af_output:/root/af_output \
    --volume <MODEL_PARAMETERS_DIR>:/root/models \
    --volume <DATABASES_DIR>:/root/public_databases \
    --gpus all \
    alphafold3 \
    python run_alphafold.py \
    --json_path=/root/af_input/fold_input.json \
    --model_dir=/root/models \
    --output_dir=/root/af_output
```

### Affected Hardware

* NVIDIA V100 GPUs
* All other CUDA Capability 7.x GPUs

***

## Incorrect Handling of Two-Letter Atoms in SMILES Ligands

<Info>
  This issue was fixed in commit [4e4023c](https://github.com/google-deepmind/alphafold3/commit/4e4023c).
</Info>

### Issue Description

Between commits [f8df1c7](https://github.com/google-deepmind/alphafold3/commit/f8df1c7) and [4e4023c](https://github.com/google-deepmind/alphafold3/commit/4e4023c), AlphaFold 3 handled incorrectly any two-letter atoms in ligands defined using SMILES strings.

### Affected Atoms

Two-letter atoms such as:

* Chlorine (Cl)
* Bromine (Br)
* Other two-letter atomic symbols

### Resolution

This issue has been resolved in the current version. If you are using an older version of AlphaFold 3, please update to the latest version or ensure you are using a commit after [4e4023c](https://github.com/google-deepmind/alphafold3/commit/4e4023c).

***

## Reporting New Issues

<Note>
  If you encounter an issue not listed here, please check the [GitHub issues tracker](https://github.com/google-deepmind/alphafold3/issues) first.
</Note>

To report a new issue:

1. Check if the issue already exists in the [issues tracker](https://github.com/google-deepmind/alphafold3/issues)
2. If not found, [create a new issue](https://github.com/google-deepmind/alphafold3/issues/new/choose)
3. Provide detailed information about:
   * Your hardware configuration
   * AlphaFold 3 version
   * Input JSON structure
   * Error messages or unexpected behavior
   * Steps to reproduce

For additional support, contact the AlphaFold team at [alphafold@google.com](mailto:alphafold@google.com).