dl_binder_design_RC

This repo provides usage instructions for setting up dl_binder_design on Penn State's Roar Collab (RC) HPC system.

Installation

1. obtain a PyRosetta license from https://els2.comotion.uw.edu/product/pyrosetta
2. Download the dl_binder_design using git clone https://github.com/nrbennet/dl_binder_design.git, and create two dirs pkgs and envs along side with it.
3. use the username and password of the newly obtained PyRosetta license to modify ~/.condarc file, also modify the path of pkgs and envs to accommodate the large number and sizes of packages.

channels: 
- https://USERNAME:PASSWORD@conda.graylab.jhu.edu
- conda-forge
- defaults
pkgs_dirs:
  - /storage/icds/RISE/sw8/dl_binder_design/pkgs
envs_dirs:
  - /storage/icds/RISE/sw8/dl_binder_design/envs

4. navigate to <base_dir>/include and run conda env create -f dl_binder_design.yml
5. once dl_binder_design env is successfully installed and activate (source activate /storage/icds/RISE/sw8/dl_binder_design/envs/dl_binder_design), install nvcc module in conda for nvcc executables: conda install -c "nvidia/label/cuda-11.3.0" cuda-nvcc
6. Install pandas: conda install pandas
7. Naviate to <base_dir>/mpnn_fr
8. Run git clone https://github.com/dauparas/ProteinMPNN.git
9. Done!