How do i solve this error in autodock tools?

Question

[zanouba.chimista]

Hi,

I am using Autodock 4.2 to dock Re-containing molecules. However, when I open the results in Autodock tools, the structure appears normal, but when I add macromolecule and use Analyze - docking - show interaction, an error massage appears:

Unable to assign HYB type to atom Re

ERROR *********************************************

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 3087, in doit self.build()

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\AutoDockTools\autoanalyzeCommands.py", line 2912, in build self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)

File "C:\Program Files(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py", line 49, in __init__ self.build(detect_pi=detect_pi)

 File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py", line 60, in build
    self.buildCloseContactAtoms(percentCutoff)              #

 File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 69, in buildCloseContactAtoms self.macro_atoms, percentCutoff=percentCutoff)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\distanceSelector.py",
line 106, in select bigC = Numeric.resize(c, (lenC, lenC, 3))

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\numpy\core\fromnumeric.py", line 615, in resize a = concatenate( (a,)*n_copies)

MemoryError

can you help me please ?

Best regards

[Joe]

This seems to suggest a memory issue (though its not a certainty). How much RAM do you have available?

[zanouba.chimista]

thank you very much for your answer RAM= 4 Go

[Joe]

That isn’t very much, especially for complicated tasks like manipulation of 3D models, I would suggest you try finding a computer with more resources.

Otherwise, try opening a model of intermediate size and see if that works, that should tell you what your RAM usage is looking like. Alternatively, observe the RAM usage in task manager or something like top if you’re on Linux, and see if it maxes out before opening your structure.

[zanouba.chimista]

okey I'll see thank you very much Mr Joe.