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It covers key workflow steps such as preparing molecular structures, choosing geometry input formats, constraining coordinates, and performing related calculations like counterpoise. The manual also explains file reading and writing, setting charge and multiplicity, cleaning and optimizing geometries, and executing both interactive and batch jobs, followed by interpreting outputs. 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All rights reserved.  \nWhile 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.  \nCanvas, 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, BioLuminate, 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.  \nSchrödinger 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, use your browser to open third_party_legal.html, which is in the docs folder of your Schrödinger software installation.  \nThis 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.  \nOctober 2015  \nContents  \nDocument Conventions ................................................................................................... xiii  \nChapter 1: Introduction ....................................................................................................... 1  \n1.1 About This Manual .................................................................................................... 1  \n1.2 Running Schrödinger Software .............................................................................. 2  \n1.3 Starting Jobs from the Maestro Interface ............................................................. 4  \n1.4 Citing Jaguar in Publications.................................................................................. 5  \nChapter 2: Running Jaguar From Maestro ........................................................... 7  \n2.1 Sample Calculation ................................................................................................... 7  \n2.2 The Jaguar Panel..................................................................................................... 10  \n2.3 The Edit Job Dialog Box......................................................................................... 11  \n2.4 Molecular Structure Input ...................................................................................... 13  \n2.4.1 Cartesian Format for Geometry Input ............................................................... 13  \n2.4.2 Variables in Cartesian Input .............................................................................. 13  \n2.4.3 Constraining Cartesian Coordinates ................................................................. 14  \n2.4.4 Z-Matrix Format for Geometry Input ................................................................. 15  \n2.4.5 Variables and Dummy Atoms in Z-Matrix Input..............................................","cbCaicxhxPA5LJkB","https://ap.wps.com/l/cbCaicxhxPA5LJkB","pdf",5526125,424,"English","# Document Conventions\n## Chapter 1: Introduction\n### 1.1 About This Manual\n### 1.2 Running Schrödinger Software\n### 1.3 Starting Jobs from the Maestro Interface\n### 1.4 Citing Jaguar in Publications\n## Chapter 2: Running Jaguar From Maestro\n### 2.1 Sample Calculation\n### 2.2 The Jaguar Panel\n### 2.3 The Edit Job Dialog Box\n### 2.4 Molecular Structure Input\n### 2.5 Reading Files\n### 2.6 Setting Charge and Multiplicity\n### 2.7 Cleaning up Molecular Geometries\n### 2.8 Writing Files\n### 2.9 Running Jobs\n### 2.10 Running Jaguar Batch Jobs\n### 2.11 Output\n## Chapter 3: Options\n### 3.1 Input Structures\n### 3.2 Basis Sets\n### 3.3 Density Functional Theory (DFT) Settings","[{\"question\":\"What does the Jaguar 9.0 User Manual explain first in the introduction section?\",\"answer\":\"It introduces the manual and explains how to run Schrödinger software, start jobs from the Maestro interface, and cite Jaguar in publications.\"},{\"question\":\"How does the manual guide molecular structure input for Jaguar?\",\"answer\":\"It describes molecular structure input and covers geometry input methods such as Cartesian format and Z-matrix format, including variables, constraints, and related calculation options.\"},{\"question\":\"Which topics are covered for running Jaguar jobs from Maestro, including batch execution?\",\"answer\":\"It covers running jobs, running Jaguar batch jobs, reading and writing files, setting charge and multiplicity, cleaning molecular geometries, and reviewing output.\"}]","Jaguar 9.0 - User Manual | PDF",1068]