Macromodel 10.8 User Manual

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Macromodel 10.8 User Manual MacroModel User Manual MacroModel 10.8 User Manual Schrödinger Press MacroModel User Manual Copyright © 2015 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, 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. 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, use your browser to open third_party_legal.html, which is in the docs folder of your Schrödinger software installation. 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. May 2015 Contents Document Conventions ..................................................................................................... xi Chapter 1: MacroModel Overview .............................................................................. 1 1.1 MacroModel User Manual ........................................................................................ 1 1.2 MacroModel ................................................................................................................ 1 1.3 MacroModel and Maestro Interaction .................................................................... 2 1.4 Calculation Preparation and Submission ............................................................. 2 1.5 Command-Line Utilities............................................................................................ 3 1.6 Running Schrödinger Software .............................................................................. 4 1.7 Starting Jobs from the Maestro Interface ............................................................. 5 1.8 Citing MacroModel in Publications ........................................................................ 7 Chapter 2: Basic Molecular Modeling ...................................................................... 9 2.1 MacroModel Force Field Implementation.............................................................. 9 2.2 Parameter Quality Considerations ....................................................................... 11 2.3 MacroModel Solvation Treatment......................................................................... 13 2.4 Truncation of Electrostatic Interactions.............................................................. 14 2.4.1 Energetics of Charges ...................................................................................... 15 2.4.2 Molecular Mechanics Description of Charge .................................................... 15 2.4.3 Bond Dipole Cutoffs (BDCO) ............................................................................ 16 2.4.4 BDCO and Molecular Modeling ........................................................................ 16 2.5 General Guidelines for Convergence .................................................................. 17 2.5.1 Minimization ...................................................................................................... 17 2.5.2 Conformational Searching ................................................................................ 17 2.5.3 Molecular and Stochastic Dynamics ................................................................. 18 2.6 Problem Size: Limits of Operation ....................................................................... 19 2.7 Nonbonded Cutoffs................................................................................................. 19 2.8 Electrostatic Treatments ........................................................................................ 20 2.9 File Conversion........................................................................................................ 20 MacroModel 10.8 User Manual iii Contents 2.10 Modified Force Field, Solvent, or Atom Type Files ......................................... 21 2.11 Hydrogen Treatment ............................................................................................. 21 2.11.1 Hydrogens on Hetero Atoms........................................................................... 21 2.11.2 Hydrogen Treatment in the AMBER* Force Field............................................ 21 Chapter 3: Running MacroModel From the Command Line................... 23 3.1 Preparing for MacroModel Calculations.............................................................. 23 3.1.1 Environment Variables ...................................................................................... 23 3.1.2 The Command File ........................................................................................... 24 3.1.3 The Command File Format ............................................................................... 24 3.1.4 The Simplified Input File ................................................................................... 26 3.2 Submitting Jobs From the Command Line......................................................... 26 3.3 Running Remote and Distributed Calculations ................................................. 26 3.4 Interacting With a Running MacroModel Job..................................................... 27 Chapter 4: General Settings ......................................................................................... 29 4.1 General MacroModel Calculation Setup.............................................................. 29 4.1.1 Specifying the Structure Input Source ......................................................... 29 4.2 The Potential Tab..................................................................................................... 30 4.3 Fixing and Freezing Atoms in Large Systems ................................................... 31 4.3.1 Methods for Freezing and Fixing Atoms ........................................................... 32 4.3.2 Freezing and Fixing Individual Atoms ............................................................... 33 4.3.3 The Substructure Facility .................................................................................. 33 4.4 The Constraints Tab................................................................................................ 35 4.4.1 Constraining Atoms, Distances, Angles, and Torsions...................................... 35 4.4.2 Freezing Atoms................................................................................................. 37 4.5 The Substructure Tab ............................................................................................. 38 4.5.1 Defining a Substructure .................................................................................... 38 4.5.2 Creating a Shell of Atoms ................................................................................. 39 4.5.3 Reading and Writing Substructures .................................................................. 40 4.6 Setting Up, Running, And Monitoring Jobs ....................................................... 41 iv Schrödinger Software Release 2015-2 Contents Chapter 5: Current Energy Calculations............................................................... 43 5.1 The Current Energy Panel...................................................................................... 43 5.2 The ECalc Tab .......................................................................................................... 43 5.3 Command File Examples ....................................................................................... 44 5.4 The Force Field Viewer........................................................................................... 46 5.5 Checking and Interpreting Results ...................................................................... 48 Chapter 6: Minimizations................................................................................................. 49 6.1 The Minimization Panel .......................................................................................... 49 6.2 Setting Minimization Parameters.......................................................................... 50 6.2.1 Minimization Methods ......................................................................................
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