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PostPosted: Fri Mar 06, 2015 11:19 am 
Millimolar User
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Joined: Fri Oct 31, 2014 12:40 pm
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So I've successfully docked several molecules with the Wild type structure of my protein. I am also interested to see if certain mutations affect the docking conformations. I use chimera to simply change one residue to another and then save it as a new pdb file.

When I load these new files into autodocktools I encounter a problem when changing the pdb into pdbqt. It simply won't do it. The error says that the index is out of range. I have noticed that when I choose the molecule to be the macromolecule instead of there simply being the protein's name (e.g. protein_name) it is in this format: u'protein_name'. I have tried working around this by making separate pdbqt files etc and loading them straight in but to no avail.

I suspect the issue is something to do with the mutation in the pdb file. Can anyone suggest a different strategy to make the mutation?

I would be very grateful for any help anyone can provide me in solving this problem.

Thank you!

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