APBS and PDB2PQR software

View the Project on GitHub Electrostatics/apbs-pdb2pqr

#Deploying and testing the PDB2PQR website

These directions are taylored for installation on OSX. Adjustments will have to be made for installation on Linux. On OSX specifically you must ensure that web sharing is enabled for the user who will be running pdb2pqr.

On your remote host:

  1. Create www directory to install pdb2pqr in. (We will use /Users/kyle/www for all examples)

  2. Create a link to this directory from /Library/WebServer/Documents

    sudo ln -s /Users/kyle/www/ /Library/WebServer/Documents/kyle

  3. edit /etc/apache2/httpd.conf to allow cgi scipts to execute in the installation directory.

On you local machine

  1. Install fabric using pip if you haven’t already.

  2. in your browser, go to remote_ip/user-name/
    • should work: list a directory
  3. clone apbs-pdb2pqr

  4. cd pdb2pqr

  5. Get the APBS libs

Currently the APBS libs are not easily compiled on any of the target platforms. These libraries can be obtained from the prebuilt executables from pdb2pqr 2.0 onward.

Internally we pass around a zip file that has the files already to go for each target platform.

  1. edit the fabric script settings file (fabfile_settings.py) in the pdb2pqr folder to target the remote machine.

If the target machine is a linux host set the “linux_host” variable to the host name of the target machine.

Likewise if the target is an OSX host set the “osx_host” variable.

You may also use @ to specify a different username for the remote host and : to specify a different port.

For instance to connect to a local linux VM which has local port 2220 redirected to 22 on the VM and the user name of “Kyle”:


To set the URL and prefix based on our example:


Deploy the site for testing

  1. run “fab deploy_and_install”

The script does the following steps: