[tools] TACC AlphaFold

Overall workflow

1. uniprot-kd得到protein seq

2. 在AF server上跑seq,下载，得到unpaired msa.a3m

3. 和tacc-2step skill说这个file，copy-rename 它到 input folder

4. 提供SMILES ，和a3m的path，准备input json files

5. 跑skill，提供密码和MFA tacc 6 digits token

另外不需要提供template，也不用让它自动搜索template("templates":null 会自动搜索，每次会去前四个cif), template只影响protein folding，不影响ligand

ssh登录

可以 ssh sky1ove@ls6.tacc.utexas.edu ，然后输入密码（google password上的），和duo push里的tacc token(6 digits)，但是每次都这样会很麻烦，这里有一个办法：

Add this to your local Mac ~/.ssh/config:

Host ls6
    HostName ls6.tacc.utexas.edu
    User sky1ove

    ControlMaster auto
    ControlPath ~/.ssh/controlmasters/%r@%h:%p
    ControlPersist 8h

    ServerAliveInterval 60
    ServerAliveCountMax 3

Then create the socket directory:

mkdir -p ~/.ssh/controlmasters
chmod 700 ~/.ssh/controlmasters
chmod 600 ~/.ssh/config

Now connect with:

ssh ls6

The first connection still asks for password/MFA. After that, new ssh, scp, rsync, or sftp connections to ls6 should reuse the existing master connection and usually won’t ask MFA again until the control connection expires or dies. SSH multiplexing reuses an existing TCP/authenticated SSH session for later sessions, avoiding repeated re-authentication. Some university HPC docs explicitly recommend this to avoid retriggering MFA for repeated SSH sessions.

For your skill, I would change the default host from:

sky1ove@ls6.tacc.utexas.edu

to:

ls6

Then use:

ssh ls6
scp file.json ls6:/scratch/10397/sky1ove/alphafold3_project/
rsync -av input_json/ ls6:/scratch/10397/sky1ove/alphafold3_project/two_step/input_json/

To keep work alive after disconnecting, use tmux inside Lonestar6:

ssh ls6
tmux new -s af3

Detach:

Ctrl-b d

Reconnect later:

ssh ls6
tmux attach -t af3

To manually close the multiplexed SSH master connection:

ssh -O exit ls6

A good wording to add to your skill:

## SSH Connection Reuse

To avoid repeated password/MFA prompts during one working session, configure local SSH multiplexing for Lonestar6. This does not save passwords, MFA tokens, or TACC credentials; it only reuses an already-authenticated SSH control connection.

Recommended local `~/.ssh/config` entry:

```sshconfig
Host ls6
    HostName ls6.tacc.utexas.edu
    User sky1ove
    ControlMaster auto
    ControlPath ~/.ssh/controlmasters/%r@%h:%p
    ControlPersist 8h
    ServerAliveInterval 60
    ServerAliveCountMax 3

Create the control socket directory:

mkdir -p ~/.ssh/controlmasters
chmod 700 ~/.ssh/controlmasters
chmod 600 ~/.ssh/config

Use ssh ls6, scp ... ls6:PATH, and rsync ... ls6:PATH instead of repeatedly typing sky1ove@ls6.tacc.utexas.edu.

For long interactive work, start tmux after logging in:

tmux new -s af3

Detach with Ctrl-b d; reattach with:

tmux attach -t af3

Close the persistent SSH master manually with:

ssh -O exit ls6
For your AF3 workflow, this is especially useful because the skill repeatedly uses SSH/SFTP/SCP-like operations while creating JSONs, copying A3M backups, submitting jobs, and checking `squeue`.
::contentReference[oaicite:3]{index=3}

目录结构

work: 存放model weight的

/work/10397/sky1ove/ls6/af3_parameters/
├── af3.bin        # 1.1 GB
├── af3.bin.zst    # 974 MB
├── chunks/        # 25 MB
└── transfer_probe.txt

scratch: 放自己的文件的

/scratch/10397/sky1ove/alphafold3_project/
├── input/
│   └── input.json
├── output/
│   └── empty
├── slurm_jobs/
│   ├── af3_test.slurm
│   ├── AF3_test.o3203127
│   └── AF3_test.e3203127
└── two_step/
    ├── manifest.csv
    ├── skipped.csv
    ├── protein_input/
    │   └── HER2.json
    ├── msas/
    │   └── HER2.a3m        # 4.9 MB
    ├── input_json/
    │   └── 20260602_HER2_yuji/
    │       └── 29 ligand JSON files
    ├── output/
    │   └── 20260602_HER2_yuji/
    │       └── empty
    ├── data_output/
    │   └── empty
    └── slurm_jobs/
        ├── af3_msa_HER2.slurm
        ├── af3_extract_HER2.slurm
        ├── af3_screen_20260602_HER2_yuji.slurm
        ├── extract_HER2_a3m.sh
        ├── AF3_msa_HER2.o3203601
        └── AF3_msa_HER2.e3203601