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Run AlphaFold2 on Tufts HPC with Command Line Interface (CLI)

This tutorial will guide the reader through the process of running AlphaFold2 on the Tufts High Performance Computing (HPC) system using the command line interface.

Prerequisites

Navigate to: https://ondemand.pax.tufts.edu/

  • Log in with your Tufts credentials
  • On the top menu bar choose Clusters->Tufts HPC Shell Access
  • Type pwd to check your current directory. You should be at your home directory, which is listed as /cluster/home/your_utln/
  • Type ls to list the files in your current directory.
  • Copy the example folder and data to your home directory by following command 
    cp -r /cluster/tufts/bio/tools/training/cas12a_af2_sp24/ ./
  • Type ls to list the files in your current directory after copying the files.

Prepare your input data

Input data for AlphaFold2 typically includes the amino acid sequences of the proteins you wish to model.

Your input data should be located here: /cluster/home/your_utln/cas12a_af2_sp24/5XUS_mut2cwf_modified.fasta
Remember to replace your_utln with your own tufts credentia

Executing AlphaFold2

Run AlphaFold2 using a command that specifies your input files, output directory, and other parameters. An example script is provided here

Remember to edit the script before you submit it to the queue
You will need to replace the path to your own path.

To submit your job to gpu node, type the following command 

sbatch /cluster/home/your_utln/cas12a_af2_sp24/script/runaf.sh

Check the results

ranked_0.pdb is your best predicted structure. This file contains the highest-ranked prediction based on the analysis, indicating it is considered the most accurate or reliable structure prediction from the set of models used. 

cd /cluster/home/your_utln/cas12a_af2_sp24/out/

[!NOTE] If you encounter any issues or this doesn't work as expected, please feel free to reach out to Shirley Li, xue.li37@tufts.edu