Thank you to Grace Baysinger from the Stanford Library for her leadership on this project and also thank you to Addis O'Connor for implementation on the Sherlock HPC cluster. Thanks also to the Vice Provost for Teaching and Learning for supporting the project and ChEM-H for providing follow up training.
Full details, including download and license instructions, can be found on the Stanford library website and the announcement from Grace:
In the coming days and weeks I will post more blog entries on how to perform analyses on your protein including electrostatic calculations, protein-protein interface analysis, disulphide engineering and antibody design. To get going here is the first installation of the tutorials showing how to do a basic analysis of protein surfaces and interfaces:
Finally for this blog, here is a quick installation guide (below the discussion panel). This is obviously a PC installation, but Mac installation is basically the same (swap the .zip file for .dmg package etc etc).
Feel free to email me with any simple problems or questions. Bugs and super technical questions should go to Schödinger tech support.
1) Request Schrödinger web account and login. Please use your Stanford email account.
2) Select an appropriate release. If you are on a PC select the 32-bit or 64-bit platform (if you have C:\Program Files (x86)\ folder on your computer you are using 64-bit windows). You can likely skip the "KNIME" workflows. Make sure you check the EULA box and agree to it.
3) Download, unzip and run "setup.exe".
4) Start the installer and select "install" ("repair" option selected below as it was already installed on my PC).
5) Select packages to install, if you are installing on a computer with limited disk space (e.g. laptop) you may only want to select "BioIluminate" (or "Maestro" if you are a chemist!). If you are installing on a computer with lots of disk space (e.g. desktop system) you can select all the packages, but beware this will take up around 8Gb of disk space.
6) When installation is complete, run "Configure Software" from the Schrödinger folder or by searching for "configure software" in the bottom windows search tool.
7) When the configuration panel pops up, select "I can identify my license server" from the pulldown menu and enter the license server hostname and port that you received from Grace Baysinger.