Hi everyone,

I’ve encountered an issue while using AutoDock Vina for docking a large protein. The initial docking steps went smoothly, but when I tried to show interactions after docking, I received the following 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)

ValueError: dimensions too large.

I suspect the error is due to the large size of the protein, as I don't encounter this issue with smaller proteins. For this particular protein, I had to set the grid box to its maximum size to encompass the entire protein.

Has anyone faced a similar issue or can provide some guidance on how to resolve this? Any help would be greatly appreciated!

Thank you!