I used the autodock4 tool for docking the aptamer and the ligand. I prepared the DNA aptamer following the process: sequence -> predict the 2d structure by MFold -> predict the 3D structure by RNAcomposer -> change the 3D RNA aptamer into 3D DNA aptamer using Discovery Studio. When I put the aptamer into autodock4, I first added the hydrogen bond, delate water and Kollman charge. But when i choose grid and macromolecular cho choose the aptamer, it always reported this problem. How can i fix this?
>>> DC1 not in qkollua; charges set to 0.0
Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 1403, in __call__
return self.func(*args)
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autogpfCommands.py", line 4479, in chooseMolecule_cb
mol = self.chooser.getMolSet()
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\Pmv\guiTools.py", line 178, in getMolSet
if self.mode=='single': return mols[0]
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\UserList.py", line 28, in __getitem__
def __getitem__(self, i): return self.data[i]
IndexError: list index out of range
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