Scientific Application – Schrodinger

Table of Contents

Overview

Setting up Environment and Invoking from a Research Computing Server

Installing Locally on a Windows Machine

Notes

Links

Additional Help

Overview

Schrodinger is a suite of molecular modeling packages that take advantage of the latest technological advances in computational chemistry. Jaguar, the high-performance ab-initio quantum mechanics application, and MacroModel, the most trusted name in molecular modeling, have been widely applied to address the full range of chemical research from materials to life sciences. Strike is a chemically aware statistical package for examining structure-property relationships. QSite is a powerful QM/MM application for studying reaction mechanisms in a variety of systems, such as protein active sites.

Also, Schrodinger provides a complete suite of software that addresses the challenges in pharmaceutical research. For structure-based drug design, Prime is an accurate protein structure prediction package; Glide performs accurate, rapid ligand-receptor docking; and Liaison predicts binding affinity. Schrodinger also provides Phase for ligand-based pharmacophore modeling, and QikProp for ADME properties prediction of drug candidates. In addition, LigPrep is a rapid 2D to 3D conversion program that can prepare ligand libraries for further computational analyses. And most recently, Schrodinger introduced CombiGlide for focused library design, and Epik for accurate enumeration of ligand protonation states in biological conditions. Finally, Maestro is the graphical user interface for all of Schrodinger’s computational programs and provides a powerful, fully-integrated molecular visualization and analysis environment.

 

Research Computing Server(s): Killdevil, Longleaf
Default Version(s): 2016-1 (Killdevil)

2016-4 (Longleaf)

Installed Version(s): 2015-1, 2015-3, 2015-4, 2016-1, 2016-2, 2016-3 (Killdevil)

2016-1, 2016-4, 2017-1, 2017-2, 2017-3, 2017-4 (Longleaf)

Setting up Environment and Invoking from a Research Computing Server

Maestro, the graphical user interface for all Schrodinger packages, can be accessed through the Research Computing server KillDevil. Choose one of the following methods for accessing Schrodinger depending on the platform.

module add schrodinger
module initadd schrodinger
  • Note. If this is your first time using Schrodinger on a Research Computing cluster you will need to create a .schrodinger/tmp directory in your personal /netscr space. To do this, log into a Research Computing cluster and then do the following two commands
cd /netscr/<onyen>
mkdir –p .schrodinger/tmp

Installing Locally on a Windows Machine

You can also install Schrodinger locally in your Windows computer. Research Computing provides the installation binary:

  • The binary for Schrodinger can be copied from Killdevil to your Windows machine from:
/nas02/apps/schrodinger-2015-1/dist/  (or whichever version you want)

Users running 32-bit Windows should copy the file: Schrodinger_Suites_2015-1_Windows.zip

Users running 64-bit Windows should copy the file: Schrodinger_Suites_2015-1_Windows-x64.zip

  • Once the zip file is downloaded, unpack the file to get installation executable.
  • Run the installation program in the unpacked directory to start installation.
  • The license file can be downloaded from:
/nas02/apps/schrodinger-2015-1/license_external
  • More information regarding installation of Schrodinger can be found in the README document in the unpacked installation directory.

Notes

  • Supported desktop for running Schrodinger is limited to Linux 2.6 only.

Links

Additional Help

Research Computing home page