I have been trying to convert pdb files of proteins into pdbqt format using Raccoon program from MGLTools-1.5.6. Some of the proteins' files have been successfully converted into pdbqt files but some throw the following error:
Exception in Tk callback
Function: (type: )
Args: ()
Traceback (innermost last):
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "raccoon.py", line 1237, in openLigand
if genPDBQT(filename, output_file):
File "raccoon.py", line 1546, in genPDBQT
if mol.returnCode is not 0:
: Protein instance has no attribute 'returnCode'
I am not able to figure out where the problem lies? is it in the Raccoon software or in the protein pdb file?
Kindly help if anyone knows the solution to it.
Thanks in advance!!
I had a similar problem. In my case, there was some problem with the geometry of input ligands. I downloaded my files from Zinc and PubChem databases; during the conversion of files from SDF to PDB using The OpenBabel software, I found some errors with ligand geometries. Then, I use the Gaussian package to amend the ligand atoms. Next, I used Raccoon, and the problem was solved. However, you can use the following tools to correct the geometry of your input ligands:
1- Avogadro is freely available for windows and Linux operating systems.
2- An online convertor that uses ChemAxon: https://datascience.unm.edu/tomcat/biocomp/convert
3- Guassian9 or 16
3- ChemBiodraw suite.
Then, you can use your ligands for docking or other computational assays. Please also check the order of your ligands bands, number of H, double-bonds, etc. Before docking analysis, you have to prepare the correct formats for obtaining high-quality results.
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