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Jaguar User Manual Jaguar User Manual Jaguar 7.9 User Manual Schrödinger Press Jaguar User Manual Copyright © 2012 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. BioLuminate, 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, LLC. 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 or its affiliates. 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. Revision A, September 2012 Contents Document Conventions ................................................................................................... xiii Chapter 1: Introduction ....................................................................................................... 1 1.1 About This Manual .................................................................................................... 1 1.2 Running Schrödinger Software .............................................................................. 2 1.3 Citing Jaguar in Publications.................................................................................. 3 Chapter 2: Running Jaguar From Maestro ........................................................... 5 2.1 Sample Calculation ................................................................................................... 5 2.2 The Jaguar Panel....................................................................................................... 8 2.3 The Edit Job Dialog Box......................................................................................... 10 2.4 Molecular Structure Input ...................................................................................... 11 2.4.1 Cartesian Format for Geometry Input ............................................................... 12 2.4.2 Variables in Cartesian Input.............................................................................. 12 2.4.3 Constraining Cartesian Coordinates................................................................. 13 2.4.4 Z-Matrix Format for Geometry Input ................................................................. 13 2.4.5 Variables and Dummy Atoms in Z-Matrix Input................................................. 15 2.4.6 Constraining Z-Matrix Bond Lengths or Angles ................................................ 16 2.4.7 Counterpoise Calculations................................................................................ 16 2.4.8 Specifying Coordinates for Hessian Refinement............................................... 18 2.5 Reading Files ........................................................................................................... 19 2.6 Setting Charge and Multiplicity ............................................................................ 20 2.7 Cleaning up Molecular Geometries...................................................................... 20 2.7.1 Quick Geometry Optimization ........................................................................... 21 2.7.2 Symmetrization ................................................................................................. 21 2.8 Writing Files ............................................................................................................. 23 2.9 Running Jobs........................................................................................................... 24 2.9.1 Output Handling ................................................................................................ 24 2.9.2 Job Submission Options ................................................................................... 25 2.9.3 Starting and Monitoring Jobs ............................................................................ 26 Jaguar 7.9 User Manual iii Contents 2.10 Running Jaguar Batch Jobs ............................................................................... 26 2.11 Output...................................................................................................................... 29 2.12 J2 Theory Calculations ........................................................................................ 29 2.13 Binding Energies of Hydrogen-Bonded Complexes....................................... 30 2.14 Fukui Functions..................................................................................................... 31 Chapter 3: Options .............................................................................................................. 35 3.1 Molecule Settings.................................................................................................... 35 3.2 Basis Sets................................................................................................................. 36 3.3 Density Functional Theory (DFT) Settings ......................................................... 41 3.4 Hartree-Fock and CIS Settings ............................................................................. 46 3.5 Local MP2 Settings ................................................................................................. 47 3.6 Generalized Valence Bond (GVB) Settings......................................................... 49 3.7 GVB-LMP2 Settings ................................................................................................ 51 3.8 SCF Settings............................................................................................................. 51 3.8.1 Accuracy Level.................................................................................................. 51 3.8.2 Convergence Criteria ........................................................................................ 53 3.8.3 Convergence Methods...................................................................................... 53 3.8.4 Orbital Treatment .............................................................................................. 54 3.9 Solvation Settings ................................................................................................... 55 3.9.1 Poisson-Boltzmann Solvation Model................................................................. 55 3.9.2 Solvation Models 8 and 6 (SM8 and SM6) ....................................................... 58 3.10 Properties ............................................................................................................... 59 3.10.1 Charges from Electrostatic Potential Fitting .................................................... 60 3.10.2 Mulliken Population Analysis........................................................................... 62 3.10.3 Multipole Moments.......................................................................................... 62 3.10.4 Natural Bond Orbital (NBO) Analysis.............................................................. 62 3.10.5 Polarizability and Hyperpolarizability .............................................................. 63 3.10.6 NMR Shielding Constants............................................................................... 64 iv Schrödinger Suite 2012 Update 2 Contents 3.10.7 Atomic Fukui Indices....................................................................................... 64 3.10.8 Stockholder Charges ...................................................................................... 65 3.10.9 Molecular Properties from SM6 and SM8 Calculations .................................. 65 3.11 Frequencies and Related Properties ................................................................. 66 3.11.1 Frequencies .................................................................................................... 66 3.11.2 Atomic Masses................................................................................................ 66 3.11.3 Scaling of Frequencies...................................................................................
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