The Molecular Graphics Laboratory Forum

This is the error i countered when splitting a mol2 file containing 651 ligands
raccoon stopped when the mol2 folder contain 648 ligands and the pdbqt contain 26
please advise
many thanks

Error: 1
<type 'exceptions.KeyError'> Exception in Tk callback
Function: <function openLigand at 0x9fd3fb4> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File "/usr/local/bin/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "/home/nic/Downloads/raccoon.py", line 1248, in openLigand
openMultiMol2(filename)
File "/home/nic/Downloads/raccoon.py", line 1334, in openMultiMol2
if genPDBQT( ligand, output_file ):
File "/home/nic/Downloads/raccoon.py", line 1540, in genPDBQT
if a.coords!=coord_dict[a]: bad_list.append(a)
<type 'exceptions.KeyError'>: <Atom instance> ZINC06494597:default:<0>:H2

Hi,

it seems there is a problem with the structure file of the ligand ZINC06494597.
Try to visually inspect it and if the structure looks correct, remove and add again the hydrogens to it.
Unless you deleted the files generated, you could simply try to import the splitted Mol2 generated by Raccoon (including the fixed ligand), instead of repeating the entire splitting procedure from the beginning.

Hope it helps,

Stefano