ADL: AutoDock problem

Shultz, Jack JShultz at
Mon Nov 5 05:11:30 PST 2007

Hi Shushan,

I've done it under cygwin, but before I run autodock I prepare all the
files. I skip the gui tools for ADT and go straight to using the python
scripts under 
C:\Program Files\MGLTools 1.4.6\MGLToolsPckgs\AutoDockTools\Utilities24
With instructions referenced here
My experience says, you need to convert all molecular files to .pdbqt
I the command shell you don't need to prefix the commands with pythonsh
this should do it. -l peptide.pdb -r receptor.pdb -r receptor.pdbqt -l peptide.pdbqt -r receptor.pdbqt -l peptide.pdbqt

Now your autodock4.exe, is did you compiled or did it come through

You can either run it from cygwin or move all the dependent cygwin dlls
to a place your application can see them. The immediate directory or
Windows directory.

First run autogrid4.exe -p GirdPArameterFile.gpf -l GridLog.glg
autodock4.exe -p GirdPArameterFile.dpf -l DockLog.dlg

That's what works for me. Let me know if and where you get errors.



-----Original Message-----
From: autodock-bounces at [mailto:autodock-bounces at]
On Behalf Of Shushan Harutyunyan
Sent: Sunday, November 04, 2007 12:14 PM
To: autodock at
Subject: ADL: AutoDock problem

Dear AutoDock support team.
I have downloaded AutoDock4 from your site and tried to dock  a ligand
(peptide) made by me with Chem3D Ultra 9.0 in .pdb extension, with a
macromolecule. I did everything as it was written in  "Using AutoDock4
With ADT" . While running AutoDock4 in cygwin I got en error message 
"assertion "finite <avg>" failed:file "", line 855
9686 [sig] autodock4 3832 C:\cygwin\usr\local\bin\autodock4.exe: ***
fatal error - called with threadlist - ix - l
I can't understand what I have done wrong. I'll be very pleased if you
give me an advice.
Best Regards,
Shushan Harutyunyan.

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