The Molecular Graphics Laboratory Forum

Hi,

I have started using Autodock Vina to calculate the binding affinity of various inhibitor compounds with our target protein. I am having some issues when trying to generate receptor pdbqt file using AutoDock Tools.

When I am trying to save the file in PDBQT format, Python Shell window pops up and shows me an error as follows
“raise AssertionError , "%s does't exist" %filename
AssertionError: 3rfa.pdbqt does't exist”

However, this command creates a pdbqt (3rfa.pdbqt) file in the same folder. I don’t face this problem when I try to make a pdbqt file for ligand. I will appreciate if you can help me fixing this issue.

I have an iron sulfur cofactor in my protein. But it looks like ADT can’t find any Gasteiger parameters for my cofactor during preparation of pdbqt file (Error message -“Sorry, there are no Gasteiger parameters available for atom 3rfa:B:SF4405:FE1”). Same thing happens for all water molecules.

I am using a version of Autodock tools called AutoDock latest (Jan 26-2015) and a MacBook Pro (Version 10.9.5).

Thanks
Arnab