Installation

OpenAWSEM installation

1. 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
   
   
2. Clone the Openawsem repository using the following command:
   
   git clone https://github.com/npschafer/openawsem.git
   
   
3. 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.
   
   
4. 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.
   
   
5. 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
   
   
6. Move the pdb_seqres.txt file to the location where you cloned the Openawsem repository.
   
   
7. 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.
   
   
8. 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
   
   
9. 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/'
   
   
10. Activate the openmm environment using the following command:
    source activate openmm
    
    
11. Install additional Python packages using the following command:
    conda install -c omnia -c conda-forge openmm pdbfixer mdtraj
    
    
12. After completing these steps, you should be able to use Openawsem on your computer.

Open3SPN2 installation

1. Activate the openmm environment using the following command:
   
   source activate openmm
   
   

2. Configure the Anaconda package manager to include the omnia and conda-forge channels. This will allow you to access the necessary dependencies from these channels. To do this, run the following commands in a terminal:

   conda config --append channels omnia
   conda config --append channels conda-forge

    

3. Install open3SPN2 using the Anaconda package manager. To do this, run the following command in a terminal:
   
   conda install -c wolynes-lab open3spn2
   Install X3DNA >= 2.4. This is necessary for open3SPN2 to run properly. To do this, follow the instructions on the X3DNA website: http://x3dna.org/

   Set the X3DNA environment variable to the location of the X3DNA installation folder. This will allow open3SPN2 to find the X3DNA executables. To do this, run the following command in a terminal, replacing /path/to/x3dna-v2.4 with the actual path to the X3DNA installation folder:

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   export X3DNA=/path/to/x3dna-v2.4
   If you want to use open3SPN2 for protein-DNA simulations, you will also need to install openAWSEM. To do this, follow the instructions on the openAWSEM website: https://github.com/npschafer/openawsem

   Add the openAWSEM path to the PYTHONPATH environment variable. This will allow open3SPN2 to import openAWSEM modules. To do this, run the following command in a terminal, replacing /path/to/openawsem with the actual path to the openAWSEM installation folder:

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   export PYTHONPATH=/path/to/openawsem:$PYTHONPATH
   If you want to install open3SPN2 locally instead of using the Anaconda package manager, you can clone the open3SPN2 repository from GitHub and install it manually. To do this, run the following commands in a terminal:
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   git clone https://github.com/cabb99/open3spn2.git
   cd open3spn2
   pip install -e .
   After completing these steps, you should be able to use open3SPN2 on your computer. Keep in mind that you will need to set the X3DNA and PYTHONPATH environment variables every time you open a new terminal or log in to your computer. If you want these variables to be set automatically, you can add the export commands to your .bashrc file. This will set the environment variables every time you open a new terminal.

Adding a location to the PATH:

1. To add a location to your PATH environment variable in Linux, you need to do the following:
   Open a terminal and run the following command to open the .bashrc file in a text editor:
   
   nano ~/.bashrc
   
   
2. Scroll to the bottom of the .bashrc file and add the following line, replacing /your/path with the location you want to add to the PATH variable:
   
   export PATH=$PATH:/your/path
   
   You can add any environment variable in a similar way:
   
   export VAR=/Some/path/
   
   Don't add spaces next to the '=' sign
   
   
3. Press CTRL + X to exit the editor, then press Y to save the changes and Enter to confirm the file name.
   
   
4. Run the following command to apply the changes to the current terminal session:
   
   source ~/.bashrc
   
   
5. Verify that the location was added to the PATH variable correctly by running the following command:
   
   echo $PATH
   
   
6. You should see the new location in the list of paths that is printed to the screen. Keep in mind that you will need to open a new terminal or log out and log back in for the changes to take effect.

Running simulations