installation.md

Installation instructions in 3 steps

Step 1 - Download ChemFlow sources.

The sources code for ChemFlow_py can be downloaded from the Github Repository.

To clone the repository:

git clone https://github.com/lmonari5/ChemFlow_py.git

Then add the ChemFlow_py scripts to your PATH and PYTHONPATH. To do so modify your ~/.bashr with your favourite text editor:

nano ~/.bashrc

Add:

export CHEMFLOW_PY_HOME="/your_path_to_ChemFlow_py"
export PYTHONPATH="${PYTHONPATH}:/${CHEMFLOW_PY_HOME}/modules"
export PATH="${PATH}:/${CHEMFLOW_PY_HOME}/modules"

Source the bashrc to update the PATH in the current terminal:

source ~/.bashrc

Remark : make sure the script you want to run are executables:

chmod +x your_path_to_ChemFlow_py/modules/chemflow.py
chmod +x your_path_to_ChemFlow_py/modules/bound_shape.py

Step 2 - Install Anaconda3 and set the environment

If you don't have Anaconda installed, follow the steps of the Anaconda Installation Guide

Then create the ChemFlow_py environment:

conda env create -n chemflowpy --file chemflowpy.yml

Remember to activate the environment before running the code

To activate the environment run:

conda activate chemflowpy

If the environment creation fails, tries these fix in order:

• set conda config --set channel_priority false
• you can find useful resources in the directory ChemFlow_py/templates/help/environment. Try again with:

  conda create -n chemflowpy --file chemflowpy_advanced.txt

• In the directory ChemFlow_py/templates/help/environment you can find 'manual_install_environment.txt'. Just open the file and run every line in the terminal

Step 3 - Install the docking/rescoring/MD programs supported

This step is quite simple: download the programs you want, make them executable and add them to the PATH.

Each program is optional

• Vina (free license):

  • Type: Docking
  • Documentation:

    https://vina.scripps.edu/manual/

  • Download:

    https://vina.scripps.edu/downloads/#

  • Make executable:

    chmod +x your_path_to_vina_folder/bin/vina

  • Add to ~/.bashrc:

    export PATH="your_path_to_vina_folder/bin:$PATH"

  • Command to run:

    vina --help

  • Requirements:

    None

• QVina2.1 (free license):

  • Type: Docking
  • Documentation:

    https://github.com/QVina/qvina

  • Download:

    git clone https://github.com/QVina/qvina.git

  • Make executable:

    chmod +x your_path_to_qvina_folder/bin/qvina2.1

  • Add to ~/.bashrc:

    export PATH="your_path_to_qvina_folder/bin:$PATH"

  • Command to run:

    qvina2.1 --help

  • Requirements:

    None

• Smina (free license):

  • Type: Docking and Rescoring

  • Documentation:

    https://sourceforge.net/p/smina/code/ci/master/tree/

  • Download:

    https://sourceforge.net/projects/smina/

    It downloads directly the executable, is adviced to put it in a specific directory

  • Make executable:

    chmod +x your_path_to_smina_folder/smina.static

  • Add to ~/.bashrc:

    export PATH="your_path_to_smina_folder:$PATH"

  • Command to run:

    smina.static

  • Requirements:

    None

• Autodock4 (free license):

  • Type: Docking and Rescoring

  • Documentation:

    https://autodock.scripps.edu/wp-content/uploads/sites/56/2022/04/AutoDock4.2.6_UserGuide.pdf

  • Download:

    https://autodock.scripps.edu/download-autodock4/

  • Make executable:

    chmod +x your_path_to_autodock/autodock4

    chmod +x your_path_to_autodock/autogrid4

  • Add to ~/.bashrc:

    export PATH="your_path_to_autodock_folder:$PATH"

  • Command to run:

    autodock4

    autogrid4

  • Requirements:

    None

• PLANTS (free academic license):

  • Type: Docking and Rescoring

  • Documentation:

    Online:

    https://www.yumpu.com/en/document/view/27077942/protein-ligand-ant-system-user-manual-for-version-11-1-

    The full PDF is available at the download page

  • Download:

    http://www.tcd.uni-konstanz.de/plants_download/

    It downloads directly the executable, is adviced to put it in a specific directory

  • Make executable:

    chmod +x your_path_to_plants/PLANTS1.2_64bit

  • Add to ~/.bashrc:

    export PATH="your_path_to_plants_folder/:$PATH"

  • Command to run:

    PLANTS1.2_64bit

  • Requirements:

    None

• AMBER (paid license, tested with Amber18):

  • Type: MD for Free Energy Rescoring

  • Documentation:

    https://ambermd.org/Manuals.php

  • Download:

    https://ambermd.org/GetAmber.php

  • Make executable: follow installation according to your version

  • Add to ~/.bashrc:

    source path_to_amber/amber.sh

  • Command to run (according to the installation):

    pmemd

    pmemd.cuda

    pmemd.cuda_SPFP

  • Requirements:

    Ambertools (free license, already included in the environment)

    Gaussian_09 (paid license) only for RESP charges:

    Add to ~/.bashrc:

    export g09root="path_to_gaussian"

    export GAUSS_SCRDIR=/tmp

    source $g09root/g09/bsd/g09.profile

• GROMACS (free license, tested with Gromacs 2021):

  • Type: MD for Free Energy Rescoring

  • Documentation:

    https://manual.gromacs.org/current/index.html

  • Download:

    https://manual.gromacs.org/current/download.html

  • Make executable: follow installation according to your version

  • Add to ~/.bashrc (in case you don't use "sudo make install"):

    export PATH="your_path_to_gromacs_build/bin/:$PATH"

  • Command to run:

    gmx

  • Requirements:

    Ambertools (free license, already included in the environment)

    CGenFF program and cgenff_charmm2gmx_py3_nx2.py (free academic license):

    Dowload and Intsallation:

     http://kenno.org/pro/cgenff/program.php
    

    replace the correspondent directories and files inside ChemFlow_py/templates/config/gromacs/cgenff