Installation Guide Installation Guide Schrödinger Suite 2011 Schrödinger Press Installation Guide Copyright © 2011 Schrödinger, LLC. All rights reserved. While care has been taken in the preparation of this publication, Schrödinger assumes no responsibility for errors or omissions, or for damages resulting from the use of the information contained herein. Canvas, CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike, and WaterMap are trademarks of Schrödinger, LLC. Schrödinger and MacroModel are registered trademarks of Schrödinger, LLC. MCPRO is a trademark of William L. Jorgensen. Desmond is a trademark of D. E. Shaw Research. Desmond is used with the permission of D. E. Shaw Research. All rights reserved. This publication may contain the trademarks of other companies. Schrödinger software includes software and libraries provided by third parties. 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September 2011 Contents Document Conventions ..................................................................................................... ix Chapter 1: Installation Notes .......................................................................................... 1 1.1 Linux Installation Process Summary..................................................................... 1 1.2 Windows Installation Process Summary .............................................................. 2 1.3 Notes............................................................................................................................ 3 Chapter 2: Hardware and Software Requirements......................................... 5 2.1 General Requirements.............................................................................................. 5 2.1.1 All Platforms........................................................................................................ 5 2.1.2 All Linux Platforms .............................................................................................. 5 2.1.3 Linux x86 32-bit executables............................................................................... 5 2.1.4 Linux x86 64-bit executables............................................................................... 6 2.1.5 Windows ............................................................................................................. 7 2.1.6 Intel Hardware..................................................................................................... 8 2.1.7 Queueing Systems.............................................................................................. 8 2.2 Disk Space for Installation....................................................................................... 9 2.3 Maestro 9.2 Requirements..................................................................................... 10 2.3.1 Graphics............................................................................................................ 10 2.3.2 Linux ................................................................................................................. 10 2.3.3 Windows .......................................................................................................... 11 2.4 Product Notes .......................................................................................................... 11 2.4.1 Canvas 1.4........................................................................................................ 11 2.4.2 Desmond 3.0..................................................................................................... 11 2.4.2.1 Queueing systems ................................................................................. 12 2.4.2.2 Network................................................................................................. 12 2.4.3 Jaguar 7.8 ......................................................................................................... 13 2.4.4 Prime 3.0........................................................................................................... 13 2.4.5 PrimeX 1.8 ........................................................................................................ 13 2.4.6 Schrödinger KNIME Extensions 1.4.................................................................. 14 Installation Guide iii Contents 2.5 Prime Third-Party Software and Databases ....................................................... 14 2.6 Documentation Requirements .............................................................................. 16 Chapter 3: Installing the Products on Linux ....................................................... 17 3.1 Access to the Software .......................................................................................... 17 3.2 Verifying System Compliance............................................................................... 18 3.3 Installing the Software and Documentation....................................................... 19 3.4 Setting the Environment Variables....................................................................... 24 3.5 Runtime Libraries.................................................................................................... 26 3.6 Enabling Hardware Stereo Viewing...................................................................... 27 3.7 Access to the Web .................................................................................................. 27 3.8 Installing Script Center Scripts............................................................................. 28 3.9 Installing Prime Third-Party Software and Databases from a Download...... 28 3.10 Installing the Prime Threading Module from a Download ............................. 31 3.11 Installing and Updating Schrödinger KNIME Extensions from the Web..... 32 3.11.1 Installing into an Existing Version of KNIME ................................................... 32 3.11.2 Adding New Schrödinger Extensions.............................................................. 34 3.11.3 Updating Existing Schrödinger Extensions ..................................................... 35 3.12 Installing VMD for Desmond ............................................................................... 36 3.13 Installing a Noncommercial Version of Desmond into an Existing Schrödinger Installation................................................................................. 37 3.14 Installing Open MPI Plugins................................................................................ 38 3.15 Setting Up Access to PyMOL.............................................................................. 38 Chapter 4: Installing the Products on Windows .............................................. 39 4.1 Installing Schrödinger Software........................................................................... 39 4.1.1 Preparing for Installation ................................................................................... 39 4.1.2 Installation Notes .............................................................................................. 40 4.1.3 Installing From the DOS Command Line .......................................................... 41 iv Schrödinger Suite 2011 Contents 4.1.4 UNC Path Checking .......................................................................................... 42 4.1.5 Troubleshooting................................................................................................. 43 4.2 Installing and Updating KNIME Extensions ....................................................... 44 4.2.1 Installing into an Existing Version of KNIME ..................................................... 45 4.2.2 Updating Existing Schrödinger Extensions ....................................................... 46 4.2.3 Adding New Schrödinger Extensions................................................................ 47 4.3 Installing Prime Third-Party Software and Databases ..................................... 49 4.4 Setting Up Access to PyMOL................................................................................ 51 4.5 Uninstalling Schrödinger Software...................................................................... 52 Chapter 5: Obtaining and Installing Licenses ................................................... 53 5.1 Determining Your License Type...........................................................................