ADL: no clusters found error

Yang Ye leafyoung at yahoo.com
Wed Oct 17 23:44:13 PDT 2007


Docking a 20aa peptide is an ambious decision, highly computational demanding. I need to remind you that AD is good at ligand docking but lacks in protein-protein docking.

I guess you may not set sufficient evaluation number limit, resulting in large indepedent result from each docking, so no cluster can be found. Anyway, you can use text editor to open the dlg file, look for "Histogram", below it you shall see the clustering result.
 
Regards,
Yang Ye



----- Original Message ----
From: IVYtony smth <ivytony at gmail.com>
To: autodock at scripps.edu
Sent: Thursday, October 18, 2007 1:48:51 PM
Subject: ADL: no clusters found error

I'm pretty new to autodock 4 and I just figured out how to run docking
computations by using ADT.

I'm trying to dock a short peptide (20 amino acids long) onto a protein
kinase that has known structure. I don't know where the binding occurs on
the kinase surface. I followed the tutorials for my docking. But when I
tried to analyze docking results by opening the docking log (.dlg) file.
However, when I click 'Analyze' -->'Conformations' --> 'Load....', I got an
error message saying: no clusters found!

I am wondering how to analyze the the docking results? visualize it? why no
clusters? I've set 'analysis' in the .dpf file.

I appreciate any reply.

Tony

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