...
- Make sure you have installed Git on your computer. This will allow you to clone the Openawsem repository from GitHub. You can download git from the following page:
https://git-scm.com/book/en/v2/Getting-Started-Installing-Git - Clone the Openawsem repository using the following command:
git clone https://github.com/npschafer/openawsem.git - Download and install STRIDE from the following link:
http://webclu.bio.wzw.tum.de/stride/
Make sure to put the STRIDE binary in your PATH, so that you can run it from the command line. - Download and install psiblast from the following link:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Make sure to put the psiblast binary in your PATH, so that you can run it from the command line. - Download the pdb_seqres.txt file from the PDB website using the following command:
wget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt - Move the pdb_seqres.txt file to the location where you cloned the Openawsem repository.
- Install conda or miniconda from the following link: https://conda.io/en/latest/miniconda.html. This will allow you to manage your Python environments and packages easily.
- Create a new conda environment called openmm that includes the necessary Python packages. To do this, run the following command:
conda create -n openmm python=3.6 biopython matplotlib numpy pandas - Set the OPENAWSEM_LOCATION environment variable to the location where you cloned the Openawsem repository.
This will allow Openawsem to find the necessary files and data. To set the environment variable, add the following command to .bashrc:
export OPENAWSEM_LOCATION='/YOUR/OPENAWSEM/DIRECTORY/' - Activate the openmm environment using the following command:
source activate openmm - Install additional Python packages using the following command:
conda install -c omnia -c conda-forge openmm pdbfixer mdtraj - After completing these steps, you should be able to use Openawsem on your computer.
...