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Desmond User Manual Desmond User Manual Desmond 4.2 User Manual Schrödinger Press Desmond 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: Introduction ....................................................................................................... 1 1.1 Installation and Configuration ................................................................................ 2 1.2 The Maestro Interface to Desmond........................................................................ 3 1.3 Desmond Calculations Overview ........................................................................... 3 1.4 Running Schrödinger Software .............................................................................. 4 1.5 Starting Jobs from the Maestro Interface ............................................................. 6 1.6 Citing Desmond in Publications............................................................................. 8 Chapter 2: Building a Model System ........................................................................ 9 2.1 Adding Solvent .......................................................................................................... 9 2.2 Setting Up the Boundary Box ............................................................................... 11 2.3 Adding a Membrane................................................................................................ 11 2.4 Using Custom Charges .......................................................................................... 13 2.5 Specifying the Force Field..................................................................................... 14 2.6 Adding Ions .............................................................................................................. 14 2.6.1 Defining an Excluded Region............................................................................ 15 2.6.2 Ion Placement ................................................................................................... 15 2.6.3 Adding a Salt..................................................................................................... 16 2.7 Running the Job ...................................................................................................... 16 2.8 Rebuilding a Model System................................................................................... 17 2.9 Quick Setup Instructions ....................................................................................... 17 Chapter 3: Running Simulations from Maestro................................................ 19 3.1 Overview of the General Desmond Panels ......................................................... 19 3.2 Selecting a Model System ..................................................................................... 20 3.3 Minimizations ........................................................................................................... 21 Desmond 4.2 User Manual iii Contents 3.4 Molecular Dynamics Simulations......................................................................... 22 3.5 Simulated Annealing Simulations ........................................................................ 24 3.6 Replica Exchange Simulations ............................................................................. 26 3.7 Metadynamics Simulations ................................................................................... 28 3.8 Simulations on Systems with Membranes ......................................................... 30 3.9 Setting Options for Desmond Simulations......................................................... 31 3.9.1 The Integration Tab ........................................................................................... 32 3.9.2 The Ensemble Tab ............................................................................................ 33 3.9.3 The Minimization Tab ........................................................................................ 34 3.9.4 The Interaction Tab ........................................................................................... 35 3.9.5 The Restraints Tab............................................................................................ 36 3.9.6 The Output Tab ................................................................................................. 37 3.9.7 The Misc Tab..................................................................................................... 38 3.10 Running a Simulation Job ................................................................................... 39 Chapter 4: Running FEP Simulations .................................................................... 41 4.1 FEP Panel.................................................................................................................. 41 4.2 Total Solvation Free Energy Calculation............................................................. 41 4.3 Selecting the FEP Protocol.................................................................................... 42 4.4 Running FEP Jobs .................................................................................................. 43 4.5 FEP Results .............................................................................................................. 44 Chapter 5: Analyzing Simulations............................................................................. 45 5.1 Viewing Trajectories................................................................................................ 45 5.2 Simulation Quality Analysis .................................................................................. 50 5.3 Protein-Ligand Interactions Analysis .................................................................. 51 5.3.1 Protein and Ligand RMSD ................................................................................ 52 5.3.2 Protein Secondary Structure Elements............................................................. 53 5.3.3 Protein RMSF ................................................................................................... 54 5.3.4 Ligand RMSF.................................................................................................... 56 iv Schrödinger Software Release 2015-2 Contents 5.3.5 Protein-Ligand Contacts ................................................................................... 57 5.3.6 Ligand-Protein Contacts ................................................................................... 58 5.3.7 Ligand Torsions................................................................................................. 59 5.3.8 Ligand Properties.............................................................................................. 60 5.4 Simulation Event Analysis..................................................................................... 62 5.5 Radial Distribution Functions ............................................................................... 63 5.6 Metadynamics Analysis ......................................................................................... 65 5.7 Replica Exchange Review...................................................................................... 66 Chapter 6: Running Simulations from the Command Line ...................... 69 6.1 The desmond Command........................................................................................ 69 6.2 Running Multiple Simulations..............................................................................
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