Welcome to Schrödinger & PyMol

 

Columbia University Libraries is happy to announce the acquisition of a site license for the renowned Schrodinger suite of molecular modeling software.  This download gives you access to the Small Molecule Drug Discovery suite, the Biologics suite, and the Materials Science suite.

A separate download for the molecular visualization program PyMol is also available -- click here for details.

On this page you will find instructions for software download and installation, as well as links to training videos and materials.  See what you can discover!

 

QUESTIONS? EMAIL digitalscholarship@library.columbia.edu



Download & Install

Here are the steps to download and install Schrodinger software in your computer:

1. If you haven't already, please create an account with Schrodinger.com.  After filling out the form, you will receive a confirmation email activating your login information.

2. Download the Suite from www.schrodinger.com/downloadcenter (you may be asked to log in with the credentials you set up in step 1)

3. Choose your desired version (usually this will be the latest available, see arrow 1 in the screenshot below)

4. Choose your operating system (see arrow 2)

5. Uncheck the KNIME Workflows box unless you know you want them (see arrow 3); otherwise this is an additional ~650 MB file that will be downloaded at the same time as the software file.

6. Click the red DOWNLOAD button.  You will be taken to a page confirming your selection.  Click on the provided link to start your download.

DSC_schrodinger_download_w_arrows

7. Once the download is finished:

Under Windows, unzip the contents of the downloaded ZIP file into a local folder (e.g. a newly created folder on the desktop) and run SETUP.EXE.  Accept all default options.  (You can also watch the Windows Quick Installation Guide)

Under Mac, open the DMG file and double-click the PKG file.  Accept all default options.  (You can also watch the Mac Quick Installation Guide)

Under Linux, watch the Linux Quick Installation Guide

8. Proceed to Configuration below before running Maestro for the first time.

 


Configuration

 

Click here to obtain the license file

 

The software will not run without it!

If you are on campus and getting a license server error, it may be because you are connected to Columbia Wi-Fi.  Please try a wired connection if available.

Before using the Schrödinger Suite, the client installation(s) must be configured to point to the license servers hosted in AWS. Make sure you have obtained a copy of the license_stub_columbiauniv_site.zip archive, which is referenced below as “the zip file”. Then, follow the specific instructions for your platform(s). Unless you have installed the Schrödinger Suite onto a shared filesystem (e.g. NFS on Linux), the following instructions must be executed on all client machines.


Note : it is assumed that the Schrödinger Suite has been installed prior to executing the following instructions.

Windows

  1. (If updating a license) Move any existing license files out of $SCHRODINGER\license\ or $SCHRODINGER\licenses\ (where $SCHRODINGER represents the installation path)
  2. Unzip the zip archive into C:\ProgramData\Schrodinger
  3. Make sure the resulting C:\ProgramData\Schrodinger\licenses directory and contents are readable by all users of Schrödinger software on the local computer
  4. (Advanced users) Unset the SCHROD_LICENSE_FILE environment variable if you have set it

 

Mac

  1. (If updating a license) Move any existing license files out of $SCHRODINGER/license or $SCHRODINGER/licenses/ (where $SCHRODINGER represents the installation path)
  2. Unzip the zip archive into /Library/Application Support/Schrodinger
  3. Make sure the resulting /Library/Application Support/Schrodinger/licenses directory and contents are readable by all users of Schrödinger software on the local computer
  4. (Advanced users) Unset the SCHROD_LICENSE_FILE environment variable if you have set it for the users of Schrödinger software

 

Linux

  1. Unzip the zip archive into $SCHRODINGER/
  2. Make sure the resulting $SCHRODINGER/licenses directory and contents are readable by all users of Schrödinger software
  3. (If updating a license) Move aside and license files at $SCHRODINGER/license (not to be confused with "licenses" from the previous step!)
  4. Unset the SCHROD_LICENSE_FILE environment variable if you have set it for the users of Schrödinger Software


Notes for Linux Installations: if you are sharing the SCHRODINGER installation via NFS and mounting on your Linux hosts, the above instructions for Linux affect all machines that mount that file system. This is most likely what you want, as it should make maintenance easier, but just be aware that changes to the license files on the shared filesystem will affect all NFS clients mounting that filesystem.

 


INSTALLATION NOTE 2020-09-17:  FOR ACCESS WHILE OFF-CAMPUS

1. Connect to the Columbia VPN (CUIT Instructions)

2. Launch the Configuration Tool (found in the installation folder) and use the “I can identify my license server” option from the “Add Licenses” drop-down menu to specify the proxy server name and port.

3. Host Name: mason.rcs.columbia.edu Port: 27008

4. Launch Maestro.

 

schrodinger_proxy_server

 

INSTALLATION NOTE 2018-08-01: If you are experiencing long delays when launching the software (2018-02 release), it is recommended that you delete the file 02_backup_server.lic from the locations listed above (i.e. the licenses directory for your operating system)


Training and Additional Resources

 


PyMol

Here are the steps to download and install PyMOL on your computer:

1. Visit this link:  https://pymol.org/dsc/ip/licen

2. Fill out the form with the info from this page; make sure to use your columbia.edu email address.

3. You will receive an email with a personalized link with access to the latest builds.  After you've logged in with your Columbia email address, you should see this page:

 

pymol_authenticated

 

4.  Click on DOWNLOAD THE LATEST PYMOL BUILDS to access the license file (see next screenshot), or try this URL: 

https://pymol.org/dsc/ip/

 

pymol_authenticated2

 

5.  Download your desired version of PyMOL from the available links

6.  With PyMOL running, go to Help, then Install New License File (see screenshot below)

6. Select the License File you downloaded in Step 2.

 

pymol_license_01