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PostPosted: Tue Aug 31, 2010 11:15 pm 
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I am unable to open my Auto Dock 4.2 docking results (.dlg file) in AutoDockTools.

The error message I get is:
Code:
 File "C:\Python25\lib\UserList.py", line 28, in __getitem__
    def __getitem__(self, i): return self.data[i]
IndexError: list index out of range


Any ideas why?

Thanks!


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PostPosted: Wed Sep 01, 2010 9:20 pm 
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Hi,

it's likely that your DLG is wrong or corrupted in some way, but without having the file is hard to tell.
Try to inspect the log file to see if there are error messages in there.


Stefano


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PostPosted: Wed Sep 01, 2010 11:37 pm 
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I'm not sure; I search for an error but found none. Nothing that says "error" anyway. At the end of the file, it says it was successfully completed...

This one may not be fixable. Its happened to multiple ligands I've used.


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PostPosted: Wed Sep 01, 2010 11:58 pm 
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The easiest way to overcome this is to re-run the docking and see if the second output is readable.

If not, for debugging this, it's important to know which version of both AutoDock and ADT you're using and at least the input ligand structure file.

Stefano


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PostPosted: Thu Sep 02, 2010 4:52 pm 
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Ok. Rerunning it didn't work.

I'm using:
ADT 1.5.4 and AutoDock4.2 (although the file name is only autodock4.exe)

The ligand is attached. I am using PyRx to run autogrid and the docking. I am docking it to a HDAC8 enzyme, which I can email you if you want. I can also send along the .dlg file that resulted from the docking.

Attachment:
AR-Phenyl-c5-HDACi.pdb [6.82 KiB]
Downloaded 235 times

Attachment:
AR_Phenyl_c5_HDACi.pdbqt [4.4 KiB]
Downloaded 237 times


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PostPosted: Fri Sep 10, 2010 6:41 pm 
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GryderArt,

could you please send the corrupted DLG files? It would be great if you could send also the parameter files (dpf and gpf) you used for creating them.

Thank you,

Stefano


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PostPosted: Fri Sep 10, 2010 8:13 pm 
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So it turns out that we were able to solve the problem. When making the ligand, I removed 2 hydrogens (that were not supposed to be added, but were) by deleting their line in the pdbqt file. This caused the ligand to be incorrectly numbered, which didn't stop it from running and completing in VINA, and didn't stop it from being "successfully completed" in AutoDock4.2, but did cause the dlg file to be unopenable. I've solved the problem now, but I've attached the files you asked for anyway if you're interested.

Thanks!!
Attachment:
HDAC8_H_add_mod4_noNa_AR-Phenyl-c5-HDACi.dpf [3.21 KiB]
Downloaded 253 times
Attachment:
HDAC8_H_add_mod4_noNa_AR-Phenyl-c5-HDACi.dlg [237.92 KiB]
Downloaded 279 times
Attachment:
HDAC8_H_add_mod4_noNa.gpf [1.17 KiB]
Downloaded 229 times


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PostPosted: Fri Sep 10, 2010 8:49 pm 
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Thank you for sharing the solution to your problem with the community!
Glad you fixed your issues,

Stefano


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PostPosted: Sat Oct 02, 2010 6:04 am 
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Gryder's results and ability to fix this problem was helpful. My group at NC State ran into something a bit similar but we overcame the problem close to the same way Gryder was able to.


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