Transcription of Using AutoDock 4 with AutoDockTools: A Tutorial
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Using AutoDock 4 with AutoDockTools: A Tutorial
1 Using AutoDock 4 with AutoDockTools: A Tutorial Written by Ru th Hu ey and Garrett M. Morris T he Sc ripp s R esea rch Ins ti tut e Mo lecula r G ra ph ics La bo ra to r y 1055 0 N. T o r re y Pi nes Rd . La Jo lla , C a lifo r nia 9 203 7-10 00 USA 8 Ja nua ry 200 8 2 Contents Co nt ent I nt rodu ct Before We FA Q Fr equ ent ly Ask ed Q ue st Looking at Dockings E xer cise O ne : Re adin g Do cking L o Procedure:..7 E xer cise T w o: Visu alizing D ock ed C onf ormat i Procedure:..10 E xer cise T hre e: Clu st erin g Conf orm at Procedure:..12 Tw o St e p QA An alysis of Aut o Do ck Re sult E xer cise F our : Visualizin g Co nf or mat io ns in C ont e Procedure:..17 Setting Up a Docking E xer cise Fi ve : P DB Files ar e Not P erf e ct : E dit ing a P DB f Procedure:..21 E xer cise Six: P re pari ng a lig and f ile f or Aut o Do Procedure.
best result is always 1_1: lowest energy cluster_best individual in cluster. Docked Energy is the sum of the intermolecular and internal energy components. Cluster RMS is the root mean square difference rms between this individual and the seed for the cluster. 1_1 is the seed for the first cluster so its Cluster RMS is 0.0.
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