AutoDock4.2_UserGuide

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1、UserGuideAutoDockVersion4.2Updatedforversion4.2.5AutomatedDockingofFlexibleLigandstoFlexibleReceptorsGarrettM.Morris,DavidS.Goodsell,MichaelE.Pique,William“Lindy”Lindstrom,RuthHuey,StefanoForli,WilliamE.Hart,ScottHalliday,RikBelewandArthurJ.OlsonModificationdate:November05,20

2、1208:37D11/P11AutoDock,AutoGrid,AutoDockTools,Copyright©1991-20091ContentsAutomatedDockingIntroduction......................................................................................................3GettingStartedwithAutoDock.............................................

3、.............................3WhatʼsNew?.....................................................................................................5Support..............................................................................................................7TheoryOverviewof

4、theFreeEnergyScoringFunction................................................8UsingAutoDockSTEP1:PreparingCoordinates........................................................................12CreatingPDBQTfileswithAutoDockTools................................................13S

5、TEP2:RunningAutoGrid...............................................................................18CreatinggridparameterfileswithAutoDockTools.....................................19STEP3:RunningAutoDock........................................................................

6、......20Choosingaprotocolforyourapplication....................................................21CreatingdockingparameterfileswithAutoDockTools...............................23STEP4:EvaluatingtheResultsofaDocking...................................................24Information

7、inthedockinglogfile...............................................................24AnalyzingdockingresultswithAutoDockTools..........................................24AppendixI:AutoDockFileFormatsPDBQTformatforcoordinatefiles..................................................

8、..................27PDBQTformatforflexiblereceptorsidechains........