!/usr/bin/env bash

SBGrid RosettaFold-All-Atom example

help@sbgrid.org

May 13, 2024

SLURM

SBATCH --mem=64G

SBATCH -t 2:00:00

SBATCH -p gpu_quad

SBATCH --gres=gpu:1

Start SBGrid environment

source /programs/sbgrid.shrc

Set version of RFAA

export ROSETTAFOLDAA_X=bf21483

Set critical env variables

export ROSETTAFOLD_DB_PATH=/programs//local/rosettafold export RFAA_DIR=/programs/x86_64-linux/rosettafoldaa/${ROSETTAFOLDAA_X}/RoseTTAFold-All-Atom

Call the correct python bundled with RFAA

python.rfaa --version

Run inference, override hydra parameters from YAML file

python.rfaa -m rf2aa.run_inference \ --config-name sbgrid_example --config-dir ./ \ checkpoint_path=${RFAA_DIR}/RFAA_paper_weights.pt \ database_params.command=${RFAA_DIR}/make_msa.sh \ database_params.hhdb=${ROSETTAFOLD_DB_PATH}/pdb100_2021Mar03/pdb100_2021Mar03