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Installation Guide 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. For details of the copyrights, and terms and conditions associated with such included third party software, see the Legal Notices, or use your browser to open $SCHRODINGER/docs/html/third_party_legal.html (Linux OS) or %SCHRODINGER%\docs\html\third_party_legal.html (Windows OS). This publication may refer to other third party software not included in or with Schrödinger software ("such other third party software"), and provide links to third party Web sites ("linked sites"). References to such other third party software or linked sites do not constitute an endorsement by Schrödinger, LLC. Use of such other third party software and linked sites may be subject to third party license agreements and fees. Schrödinger, LLC and its affiliates have no responsibility or liability, directly or indirectly, for such other third party software and linked sites, or for damage resulting from the use thereof. Any warranties that we make regarding Schrödinger products and services do not apply to such other third party software or linked sites, or to the interaction between, or interoperability of, Schrödinger products and services and such other third party software. 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...........................................................................
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