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README.md

README.md

VirtualScreening

Introduction

VirtualScreening is a Python package inheriting from pymdsetup to perform virtual screening on a set of predefined targets.

Version 1.0

This version is just an example of a functional workflow. VirtualScreening protocol uses the following applications:

  1. GROMACS: Open source and widely used molecular dynamics simulation package. (http://www.gromacs.org/)
  2. SCWRL4: Application to determine the protein side chain conformations. (http://dunbrack.fccc.edu/scwrl4/)
  3. GNUPLOT: Gnuplot is a portable command-line driven graphing utility for Linux (http://www.gnuplot.info/)
  4. PyCOMPSs (optional just for parallel executions): Python library for parallel computing. (https://www.bsc.es/computer-sciences/grid-computing/comp-superscalar/programming-model/python)
  5. ACPYPE (optional) and AMBERTOOLS

Offline Installation: Using Anaconda

https://www.anaconda.com/
(Assuming that you already installed GROMACS, SCWRL4 and GNUPLOT)

  1. On your local connected computer, download Pymdsetup, Anaconda and the Biopython Anaconda package and copy them to the offline computer:

    git clone https://github.com/bioexcel/virtualscreening.git
    wget https://repo.continuum.io/archive/Anaconda2-5.1.0-Linux-x86_64.sh
    wget https://repo.continuum.io/pkgs/free/linux-64/biopython-1.69-np113py27_0.tar.bz2
  2. On the disconnected computer:

    bash Anaconda2-5.1.0-Linux-x86_64.sh
    source .bashrc
    mv biopython-1.69-np113py27_0.tar.bz2 nose-1.3.7-py27_1.tar.bz2 ~/anaconda2/pkgs/
    conda create -n vsenv python=2.7
    source activate vsenv
    conda install --use-index-cache --use-local --offline  numpy pyyaml requests nose
    conda install ~/anaconda2/pkgs/biopython-1.69-np113py27_0.tar.bz2
    echo "~/virtualscreening" > ~/anaconda2/envs/vsenv/lib/python2.7/site-packages/virtualscreening.pth

Online Installation: Using APT and PIP

(We are assuming that you are installing VirtualScreening in your home directory cd ~)

  1. Install CMAKE and GNUPLOT:

    sudo apt-get -y install git vim htop cmake gnuplot
  2. Install numpy biopython pyyaml requests and nose Python libraries:

    sudo pip install --upgrade pip
    sudo pip install numpy biopython pyyaml requests nose
  3. Clone the project and add the project path to the PYTHONPATH variable:

    git clone http://mmb.irbbarcelona.org/gitlab/bjimenez/virtualscreening.git
    export PYTHONPATH=~/virtualscreening:$PYTHONPATH
    #If you want to make this change permanent in your .bashrc file:
    echo "export PYTHONPATH=~/virtualscreening:\$PYTHONPATH" >> ~/.bashrc
  4. Register in http://dunbrack.fccc.edu/scwrl4/license/index.html, download the "install_Scwrl4_Linux" executable file, run the following commands:

    chmod u+x install_Scwrl4_Linux
    ./install_Scwrl4_Linux

And follow the SCWRL4 interactive installation instructions.

  1. Download and install GROMACS 5.1:

    wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.2.tar.gz
    # From the 5.1.2 Gromacs install guide
    # http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html
    tar xfz gromacs-5.1.2.tar.gz
    cd gromacs-5.1.2
    mkdir build
    cd build
    cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
    make
    make check
    sudo make install
    source /usr/local/gromacs/bin/GMXRC
    #If you want to make this change permanent in your .bashrc file:
    echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bashrc
  2. Install AutoDockVina and MGLTools:

    sudo apt-get install autodock autodock-vina autodocktools autogrid
    cd $HOME/bin
    wget http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz
    tar zxvf mgltools_x86_64Linux2_1.5.6.tar.gz
    cd mgltools_x86_64Linux2_1.5.6
    ./install.sh
    echo "source $HOME/mgltools_x86_64Linux2_1.5.6/initMGLTools.sh" >> ~/.bashrc
  3. Install OpenBabel:

    sudo apt-get install openbabel python-openbabel
  4. Install AMBERTOOLS and ACPYPE:

    wget http://ambermd.org/downloads/install_ambertools.sh 
    bash install_ambertools.sh -v 3 --prefix $HOME --non-conda 
    echo "source $HOME/amber17/amber.sh" >> ~/.bashrc
    
    sudo pip install acpype

Copyright & Licensing

This software has been developed in the MMB group (http://mmb.pcb.ub.es) at the BSC (http://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission (EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

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