Alphafold is only avaiable on Wahab
To use alphafold, please use job script below as a template:
#!/bin/bash
#SBATCH -c 8
#SBATCH -p gpu
#SBATCH --gres gpu:1
module load container_env alphafold
run_alphafold ARGUMENTS
Complete the job script above and submit it with sbatch command. Click here for more information on Job Submission.
Following arugment should be supply to the run_alphafold command:
model_preset
--model_preset="pick one from below"
monomer # monomer model
monomer_casp14 # monomer model with extra ensembling
monomer_ptm # monomer model with pTM head
multimer # multimer model
fasta_paths
--fasta_paths="path to the input fasta file"
Path to your input, it should be in .fasta format
output_dir
--output_dir="path to the output directory"
max_template_date
--max_template_date="a date"
Maximum template release date to consider. Important if folding historical test sets.
When unsure, try "2022-06-01"
module load container_env alphafold
run_alphafold --helpfull
A complete job script should looks like:
#!/bin/bash
#SBATCH -c 8
#SBATCH -p gpu
#SBATCH --gres gpu:1
module load container_env alphafold
run_alphafold \
--model_preset=monomer \
--fasta_paths=/home/john_doe/input.fasta \
--output_dir=/home/john_doe/output \
--max_template_date="2022-06-01"