I had set an autodock run for docking an atp molecule to a kinase enzyme. I had set the number of GA runs to 1000. But, after the dock run had completed and I try to analyze the .dlg file, I am hit by the following error in the IDLE shell.The error is given below. Can someone explain why I am experiencing the error for the past few consecutive runs?
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
result = command( *args, **kw )
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autoanalyzeCommands.py", line 3852, in doit
d.readDlg(dlgFile)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\Docking.py", line 96, in readDlg
dlo = DockingLogObject(self, dlgFile)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\Docking.py", line 728, in __init__
parser.parse(filename)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\DlgParser.py", line 107, in parse
self.match(allLines)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\DlgParser.py", line 220, in match
apply(d['func'], (lines,), {})
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\DlgParser.py", line 718, in getModelLines
self.makeModels(modelList)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\DlgParser.py", line 814, in makeModels
clist.append(self.makeModel(curMod))
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\DlgParser.py", line 838, in makeModel
d['run'] = int((ll)[3])
ValueError: invalid literal for int() with base 10: 'C:/Users/acer/Desktop/17.11.2016/Run1/dock.dpf'
This is bug. You need to find solution with Google search.
Alternatively, what I will suggest is installation of ADT in a different computer and analyse your results there.
@Rajiv Kumar Kar : I had googled it and found that few had reported the same problem but with no solution. I had tried installing ADT in another gear and analyzing the same but found the error repeatedly haunting, irrespective of the system.
Check configuration. Try I3 or I5 processor, if using windows or try Ubuntu 64 bit. Don't worry, it will work!
Thank you Rajiv sir. I am currently running the software in Ubuntu os and the processor is 15 and octa core. I made an analysis of the dlg file and have found that the run was successful and complete. The problem lies in dlg file input to the autodock software for analysis. I even tried analyzing the dlg file in a windows os but in vain.
you could use analyzer via python scripts which located in Utilities24. it works well without any error. However, it's not the graphic user interface.
mgltools.scripps.edu/api/AutoDockTools/AutoDockTools.Utilities24-module.html
Orathai Mam. Thank u for the response. I would be really helpful if u would provide information on how to use the utilities24 module.
Did you solve the problem? if not use PyRX for AutoDock. The file conversion is automatic and error free. Looking into the error mentioned above it is the problem with docking result analyse module. Rather than 1000 runs, check with 10 runs at first instance. Attach dlg also, it helps is solving the problem.
I understand that this is an old post; however, i hope that i can help people in the future. This error is caused by your use of RUN in the path of your file, i.e.:
C:/Users/acer/Desktop/17.11.2016/Run1/dock.dpf
The code recognizes Run as a command and tries to process it. Just Make sure that the word Run doesn't appear and you should be fine.
Best regards,
Dear Sasidharan,
This problem is very easy to solve
You must create your research folder on drive C.
for example
C: \ new
(Do not create in C:\Users\alion\Desktop\new)
Good luck
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