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Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C. All rights reserved. Schrödinger, FirstDiscovery, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Prime, QSite, and QikProp are trademarks of Schrödinger, L.L.C. MacroModel is a registered trademark of Schrödinger, L.L.C. To the maximum extent permitted by applicable law, this publication is provided “as is” without warranty of any kind. This publication may contain trademarks of other companies. October 2003 Contents Chapter 1: Introduction.......................................................................................1 1.1 Conventions Used in This Manual.......................................................................2 1.2 Citing Jaguar in Publications ...............................................................................3 Chapter 2: The Maestro Graphical User Interface...........................................5 2.1 Starting Maestro...................................................................................................5 2.2 The Maestro Main Window .................................................................................7 2.3 Maestro Projects ..................................................................................................7 2.4 Building a Structure.............................................................................................9 2.5 Atom Selection ..................................................................................................10 2.6 Toolbar Controls ................................................................................................11 2.7 Mouse Functions................................................................................................14 2.7.1 Mouse Functions in the Workspace .......................................................14 2.7.2 Mouse Functions in the Project Facility.................................................15 2.8 Shortcut Key Combinations...............................................................................16 2.9 Undoing an Operation........................................................................................17 2.10 Maestro Command Scripts...............................................................................17 2.11 Specifying a Maestro Working Directory........................................................18 2.12 Running and Monitoring Jobs..........................................................................19 2.13 Help..................................................................................................................20 2.14 Ending a Maestro Session................................................................................21 Chapter 3: Running Jaguar From Maestro .....................................................23 3.1 Sample Calculation............................................................................................23 3.2 Molecular Structure Input..................................................................................26 3.2.1 Entering or Editing a Geometry Using the GUI.....................................26 3.2.2 Cartesian Format for Geometry Input ....................................................28 3.2.3 Variables in Cartesian Input ...................................................................28 3.2.4 Constraining Cartesian Coordinates.......................................................29 3.2.5 Z-Matrix Format for Geometry Input.....................................................29 3.2.6 Variables and Dummy Atoms in Z-Matrix Input ...................................31 3.2.7 Constraining Z-Matrix Bond Lengths or Angles ...................................32 3.2.8 Counterpoise Calculations .....................................................................32 3.2.9 Specifying Coordinates for Hessian Refinement ...................................32 3.3 Charge and Multiplicity (State) .........................................................................33 Jaguar 5.5 User Manual iii Contents 3.4 Reading Files .....................................................................................................34 3.4.1 Reading in Geometries Only..................................................................34 3.4.2 Reading in Geometries and Job Settings................................................35 3.4.3 Read as Geometry 2 or Geometry 3 Settings .........................................35 3.5 Cleaning up Molecular Geometries ...................................................................36 3.5.1 Quick Geometry Optimization...............................................................36 3.5.2 Symmetrization ......................................................................................37 3.6 Running Jobs......................................................................................................38 3.6.1 Starting Individual Jobs..........................................................................38 3.6.2 Running Batch Jobs or Scripts ..............................................................40 3.7 Saving Input Files ..............................................................................................44 3.8 Output ................................................................................................................45 3.9 Other Maestro Features......................................................................................46 3.9.1 Checking Jobs With the Monitor Panel..................................................46 3.9.2 The Reset Option....................................................................................46 3.9.3 Editing Input...........................................................................................46 3.9.4 The About and Help Buttons..................................................................47 3.9.5 Closing the Jaguar Panel ........................................................................48 3.9.6 Other Jaguar Panel Options....................................................................48 Chapter 4: Options .............................................................................................49 4.1 Density Functional Theory (DFT) Settings .......................................................49 4.1.1 Stage and Grid Density ..........................................................................50 4.1.2 DFT Model Options ...............................................................................51 4.1.3 Custom Functionals................................................................................53 4.2 Local MP2 Settings............................................................................................54 4.2.1 Summary of the LMP2 Method in Jaguar..............................................54 4.2.2 Setting up an LMP2 Calculation ............................................................55 4.3 Generalized Valence Bond (GVB) Settings.......................................................56 4.3.1 GVB or GVB-RCI Pair Input.................................................................57 4.4 GVB-LMP2 Calculations ..................................................................................57 4.5 Solvation ............................................................................................................58 4.5.1 Solvent Parameters.................................................................................59 4.5.2 Performing or Skipping a Gas Phase Optimization ...............................60 4.6 Properties ...........................................................................................................60 4.6.1 Electrostatic Potential Fitting.................................................................60 4.6.2 Multipole Moments................................................................................62 4.6.3 Polarizability and Hyperpolarizability ...................................................62 4.6.4 Electron Density.....................................................................................63 iv Jaguar 5.5 User Manual Contents 4.6.5 Mulliken Population Analysis................................................................64 4.6.6 Natural Bond Orbital (NBO) Analysis...................................................64 4.7 Frequencies and Related Properties...................................................................64 4.7.1 Frequencies ............................................................................................65 4.7.2 Atomic Masses .......................................................................................66 4.7.3 Scaling of Frequencies ...........................................................................66 4.7.4 Animation of Frequencies ......................................................................67 4.7.5 Infrared Intensities .................................................................................69 4.7.6 Thermochemical Properties ...................................................................69 4.8 Basis Set.............................................................................................................70 4.9 Methods .............................................................................................................74 4.9.1 Wavefunction Type (Restricted or Unrestricted)....................................74 4.9.2 Selecting Electronic States.....................................................................75 4.9.3 Choosing an Initial Guess Type .............................................................76
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