Allows control for fibril design pipeline through single config file.

Fetch pdb -> chain renaming based on 3D coordinates(since only takes one fibril), res_num renumbering, pyrosetta fast-relax -> mpnn formatting and config file -> submit

Overall Proces 'git clone (https://github.com/Chen-Jie7/fibril_pipeline.git)'

0. If you don't have a conda installed, would recommend getting mamba(bascially same thing as conda)

   • Follow instructions at (https://github.com/conda-forge/miniforge)

1. Running ProteinMPNN Once time Setup Instructions 0. cd to fibril_pipline

   1. 'git submodule init'
   2. 'git submodule update'
   3. 'mamba env create -n environment.yml'
   4. 'mamba install pytorch torchvision torchaudio cudatoolkit=11.8 -c pytorch' or go to (https://pytorch.org/) for newest cuda version
   5. install pyrosetta a. pip install pyrosetta-installer==0.1.1 b. python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta(mirror=1)'

   Notice!:

   • Make sure to change all the paths to your own!
   • Only one phase can be run at a time

   Verify run

   • Change mpnn_config.yml
   • python 1_run_mpnn.py
   • This will run the current 7ymn sample based on mpnn_config file spcifications.

2. Energetic Calculations Config setting in Phase 3 to parallelize energetic calculations and saving those pdbs

3. Running Upside2

   1. git clone https://github.com/sosnicklab/upside2-md.git
   2. cd upside2-md
   3. ./install.sh
      • Here you might get a little upside install bug problem where it says can't find eigen3 0. mamba activate upside2
        1. $CONDA_PREFIX -name "Macros.h" 2>/dev/null
        2. Copy paste the full path that ends with 'include/Eigen/src/Core/util/Macros.h'
        3. Go to upside2-md/cmake/FindEigen3.cmake
        4. Ctrl f to find 'file(READ "${EIGEN3_INCLUDE_DIR}/Eigen/src/Core/util/Macros.h" _eigen3_version_header)'
        5. Replace it with 'file(READ "[Your path above]" _eigen3_version_header)' Example: file(READ "/work/CAND/shared/Chens/miniforge3/envs/upside2/include/Eigen/src/Core/util/Macros.h" _eigen3_version_header)