Using AutoDock with AutoDockTools - Scripps Researchwww.researchgate.net › post › attachment › download

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Contents

Co ntents .......................................................................... 2 Introdu ction ..................................................................... 4 Before We Start….............................................................................4 FA Q – Fr equ ently Ask ed Q ue stions ..................................... 5 Exer cise O ne : P DB Files ar e Not Perfe ct: E diting a P DB file ... 7 Procedure: .......................................................................................7 Exer cise T w o: Pr ep aring a ligan d file for Auto Do ck. ............ 11 Procedure: .....................................................................................11 Exer cise T hre e: Pr ep arin g th e m acr om olec ule file. .............. 15 Procedure: .....................................................................................15 Exer cise F our : Pre pari ng t he grid par am eter f ile. ................ 17 Procedure: .....................................................................................17 Exer cise Fi ve : Startin g Aut oGri d ....................................... 20 Procedure: .....................................................................................20 Exer cise Six: Pre pari ng th e do cking p ara met e r file. ............. 22 Procedure: .....................................................................................22 Exer cise Sev en : Starti ng Auto Do ck. .................................. 24 Procedure: .....................................................................................24 Exer cise Eight : Analyzi ng Auto D ock R esults -R eadi ng D ockin g Logs .............................................................................. 26 Procedure: .....................................................................................26 Exer cise Ni ne: A nalyzi ng Auto Do ck Re sults -V isualizing D ock ed Co nform ation s ................................................................ 29 Procedure: .....................................................................................29 Exer cise T en : Analyzi ng Auto Do ck Re sults -Cl usterin g Co nform ation s ................................................................ 31 Procedure: .....................................................................................31 Tw o Ste p QA An alysis of Auto Do ck Re sults ......................... 34

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Exer cise Ele ven : An alyzing Auto D ock R esults -Vis ualizing Co nform ation s in C ont ext ................................................. 36 Procedure: .....................................................................................36 Files for e xer cise s: .......................................................... 40 Input Files:......................................................................................40 Results Files ....................................................................................40 Useful Scripts..................................................................................40 Customization Options for ADT ........................................................40 App en dix 1: D ockin g P aram eter s ...................................... 41 Parameters common to SA, GA, GALS: ............................................41 Simulated Annealing Specific Parameters:.........................................43 Genetic Algorithm Specific Parameters: ............................................44 Local Search Specific Parameters: ....................................................45 Clustering keywords:.......................................................................46 App en dix 2: C onfor matio n Play er ..................................... 47

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Introduction

This tutorial will introduce you to docking using the AutoD ock suite of programs. We will use a Graphical User Interface called Auto Doc kT ool s , or ADT , that helps a user easily set up the two molecules for docking, launches the external number crunching jobs in Auto Doc k , and when the dockings are completed also lets the user interactively visualize the docking results in 3D.

Before We Start… And only if you are at The Scripps Research Institute… These commands are for people attending the tutorial given at Scripps. We will be starting the graphical user interface to AutoDock from the command line. To do this, you need to open a Terminal window and then type this at the UNIX, Mac OS X or Linux prompt: % alias adt /mgl/prog/share/bin/adt14 % source /tsri/python/share/bin/initadt_v2.csh % limit stacksize unlimited % cd tutorial % adt

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FAQ – Frequently Asked Questions

1. Where should I start ADT? You should always start ADT in the same directory as the macromolecule and ligand files. You can start ADT from the command line in a Terminal by typing “adt ” and pressing or . 2. Should I always add polar hydrogens? Yes, for the macromolecule you should always add polar hydrogens and then assign Kollman United Atom charges. For the ligand, you should add all hydrogens before computing Gasteiger char