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Macromodel User Manual MacroModel® Interactive Molecular Modeling System Version 7.0 MacroModel User Manual © 1999 Schrödinger, Inc. All rights reserved. Derived from material which is © Columbia University Table of Contents User Manual Table of Contents CHAPTER 1 MacroModel Overview 9 1.1 Conventions Used in This Manual 9 1.2 New Features 11 1.3 General Information 13 CHAPTER 2 Input Mode and General Operation 15 2.1 MacroModel Windows 15 Message Window 16 Main Structure Window 17 Main Button Panel 18 Mode Options Window 18 Submode Options Window 19 Control Window 20 Popup Prompt 20 Help and Documentation 20 Structure Input 22 Atom Picking 22 SYSTEM 23 OSF/Motif Window Manager 23 Structure File Reading and Writing 24 File Reading 25 File Writing 27 Foreign Structure Files 28 Compressed MacroModel Files 29 2.2 MacroModel 2D: X-Windows (Two-Dimensional) Operation 29 Global XY Translations 30 Global XY Rotations 30 Scaling and XY Clipping 31 X Emulators 31 2.3 MacroModel 3D: GL (Three-Dimensional) Operation 32 Scaling and XY Clipping 32 Operation of the 3-Button Mouse 32 Global Transformations 33 Global Rotation - Rot X, Rot Y, Rot Z Buttons 34 Global Centering and Translation - Right Mouse Button. 35 MacroModel User Manual Version 7.0 3 Table of Contents Zooming, Clipping Planes and Depth Cueing - Control Window. 36 Torsion Angle Rotations 37 Specific Torsion Angle Setting - ROTAT Button 38 Real Time Torsional Rotations - Rot T Button 38 Molecular Translations and Rotations (Docking) 40 Incremental Translations and Rotations - Orient Sub- mode 41 Real Time Molecular Translations and Rotations - TR- Mol Button 42 Monitoring Geometrical Changes 43 Monitoring Specific Distances and Angles - ADist, BAngl and DAngl Buttons 43 Bump Checking - Opt Button 44 Structural Rendering Options 45 Wire Frame Line Diagrams 45 Polytube Diagrams - Polytube Button 46 Ball-and-Stick and CPK Space-filling Diagrams - Ball-and-Stick and CPK Buttons 46 Stereo - Stereo button 47 Hardware Stereo 47 Setting MacroModel Colors - Set Colors 48 Resizing of CPK spheres - CPK Resize 48 2.4 Structure Building 49 Modifying Existing Structures 50 Structure Files from External Sources 51 Manual Molecular Construction 52 Conformationally Flexible Molecules 53 Molecular Complex Construction and Docking 53 Renaming Facility - Renam 54 Extended Atom Types 56 CHAPTER 3 Energy Mode and Operation with BatchMin 57 3.1 MacroModel Force Fields 57 Differences in force field equations 58 Differences in parameters 59 3.2 Solvation Treatment 61 3.3 Convergence 62 Running Energy Calculations with MacroModel/ BatchMin 62 4 MacroModel User Manual Version 7.0 Table of Contents 3.4 Setting Up BatchMin Energetic Jobs 63 Running Old Command Files 63 Examining BatchMin COM Files 64 Multiple BatchMin Operations - NxtOp Button 64 3.5 Starting BatchMin Energetic Jobs 65 3.6 Monitoring BatchMin Energetic Tasks 68 3.7 Terminating BatchMin Energetic Tasks 69 3.8 Halting BatchMin Tasks 69 3.9 Putting BatchMin Tasks to Sleep 69 3.10 BatchMin Communication File Disposition 70 3.11 Typical BatchMin Energetic Tasks 70 Energy or Gradient Calculation 71 Button Description of operation 71 Full Structure Energy Minimization 71 Button Description of operation 71 Substructure Energy Minimization 73 Button Description of operation 73 Molecular, Stochastic Dynamics And Mixed Mode 75 Conformational Searching - Monte Carlo Method (MCMM) 77 3.12 FFVIEW: Force-field parameter viewer/editor 79 Interaction display panels 80 Viewing the force-field 82 Editing the force-field 82 CHAPTER 4 Analyze Mode 85 4.1 Internal Coordinate Monitors - ADist, BAngl, DAngl 86 4.2 Atom Numbers - FAtm, NAtm, FRes, NRes, Num, Clear 86 4.3 Textual Captions - AddLb 87 4.4 Averaged Atom Positions or Centroids - AveAt 87 4.5 Multiple Conformation Filtering - Filtr 88 4.6 Multiple Substrate Docking via a Dock File - DFile 90 4.7 Dot Surfaces - SURFAC submode 90 4.8 Contour Panel (Ramachandran Plots) - Cntr 91 4.9 Plotting of torsion angle - energy profiles - Plot1D 94 Main Controls 94 Interacting with the plot 97 Changing the Plot Appearance 98 4.10 Structure Plotting - Plot 98 Wireframe 99 MacroModel User Manual Version 7.0 5 Table of Contents PixelMap 99 Other 100 4.11 Boolean Operations on Atom Sets - ABool 101 4.12 Volume Boolean Operations On Molecules - MBool 102 4.13 Ribbn (Ribbon Panel) 103 4.14 Movie 105 4.15 Hydrogen Bonding (Hbond, HPref Buttons) 105 4.16 Photo Mode 106 4.17 ASL (Atom Specification Language) Panel 106 The Buttons 106 Commands (classes) and Properties 106 Operators 107 Operator Priority (decreasing priority) 107 Full Descriptions of Commands 108 Abbreviations/Aliases 109 Some Examples 109 Notes 110 CHAPTER 5 Other Programs 111 5.1 Xrbm 111 Overview 111 Running xrbm 111 Monitoring a BatchMin job 112 Button Descriptions 112 Troubleshooting 113 Appendix 1 Installing MacroModel 115 MacroModel Directory Structure 115 Environment Variables 115 INClude directory paths 116 Silicon Graphics Installation 116 IBM RS/6000 Installation 118 Appendix 2 MacroModel on a Macintosh or PC 121 Macintosh 121 Using MacX 122 PC 124 6 MacroModel User Manual Version 7.0 Table of Contents Appendix 3 Setting Up MacroModel and BatchMin Communica- tion 125 Summary 125 How To Install Entries In hostfiles.dat 126 Adding Entries For Locally Executing Jobs 126 Troubleshooting 127 Symptoms 127 Actions 128 NFS Style Remote BatchMin Installation Instructions 128 How the NFS Style Remote BatchMin Facility Works 128 How to install entries in hostfiles.dat 128 Establishing a shared directory with NFS 129 Notes 133 BatchMin Network Server Installation Instructions 134 Overview 134 Installation 135 Conventions 135 Step1: Informing inetd 136 Step 2: Get rsh running 139 Step 3: Try Out rbm and ’jump start’ the daemon 139 Step 4 (Optional): MacroModel -- Accessing the Serv- er From the Graphical User Interface 140 Some Final Notes 141 Trouble Shooting 141 Using the RPC Network Connection to Run BatchMin Manually 143 Installing Additional BatchMin Network Server Services 144 BatchMin Force Field, Solvent and atom.typ Files 145 Configuring bminrd, the BatchMin Network Server, to Start Automat- ically at Boot Time on an SGI 146 Appendix 4 MacroModel Atom and Bond Types 147 BONDS 147 ATOMS 148 Appendix 5 MacroModel Structure File Format 153 MacroModel Uncompressed File Format 154 Entry Header Line (first line of file or entry) 154 Atom Entries 154 MacroModel Atom Color Table 155 MacroModel/PDB Residue Types 156 MacroModel User Manual Version 7.0 7 Table of Contents MacroModel Compressed Entry Format 157 Entry Header Line (first line of file or entry) 158 Atom Entries 158 User Manual Index 159 8 MacroModel User Manual Version 7.0 CHAPTER 1 MacroModel Overview MacroModel V7.0 is the 1999 UNIX, X-Windows and GL release of Macro- Model. At this time, V7.0 will run with real-time, three-dimensional (3D) graph- ics on Silicon Graphics workstations (IRIX 6.5.2 or later operating system required), and on IBM RS/6000 workstations having Z-buffering, 24-bit IBM GL (not OpenGL) graphics, and the AIX 4.3.2.0 or later operating system. It will also run with small molecule real-time rotation (two-dimensional, i.e. 2D operation) using X-windows displays on a range of X-terminals including X-Terminals, X Windows-only workstations, and Macintosh and PCs running X Server emulators. 1.1 Conventions Used in This Manual This manual uses the following conventions: • courier font identifies program output listings. • bold courier font identifies items the user should type in verbatim. It is also used to denote file names, e.g. mystructure.dat. • italic courier font identifies things the user should replace when typing e.g. % ls filename • HELVETICA font indicates the names of MacroModel Motif Panels and Titles of Sections in the panels. • HELVETICA BOLD font indicates the names of MacroModel menu buttons and push buttons. MacroModel User Manual Version 7.0 9 CHAPTER 1: MacroModel Overview • N.B. If you are viewing this document using HTML, the fonts will probably not appear as Courier or Helvetica; either way, however, they will appear as they do in the preceding paragraph. • <> indicates something that should be replaced, e.g. ls <filename>. • [] indicates something that is optional. That is, it one may choose to include or not include the item, e.g. ls [-l]. • This icon indicates instructions which will result in an error if not followed correctly. • This icon identifies items of special interest for novice users. New • This icon is used to indicate a feature which is new in the current version of MacroModel. • This icon is used to indicate a feature only available in the 3D version of 33DD MacroModel • This icon is used to indicate a feature only available in the 2D version of 2D MacroModel 10 MacroModel User Manual Version 7.0 References to some environment variables are made throughout this manual. The environment variables and their default location are as follows: VARIABLE VALUE MMOD_ROOT Directory where MacroModel was loaded from tape (e.g. /usr/people/mmod) MMSITEDIR $MMOD_ROOT/run/mmdat MMEXECDIR $MMOD_ROOT/run/exec Table 1. MacroModel Environment Variables When one of these variables appears in the text it is used to represent the value that is assigned to it (typically a directory path). 1.2 New Features MacroModel V7.0 has a few enhanced capabilities relative to V6.5 , however our recent efforts on the graphical user interface side of MacroModel have been con- centrated on the development of Maestro. The major enhancements on the front- end of MacroModel 7.0 are bug fixes, as well as features that allow access to some of the new BatchMin methods. Below are a few of the enhancements for MacroModel: • OPLS-AA force-field now available MacroModel User Manual Version 7.0 11 CHAPTER 1: MacroModel Overview • Atom replacement changed to not alter PDB residue, PDB atom name, MacroModel residue name when changing an atom type doesn’t change the element type.
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