ADL: "Unknown or inappropriate tag" Error in Vina for Protein File

Jatin Kashyap jk435 at
Thu Sep 3 21:02:17 PDT 2020

Dear AutoDock Community,

Please redirect me if I am posting to the wrong email list. I am getting a file format error in the Vina docking run.[1] I am taking a protein and trimming it in PyMol followed by minimization on YASARA server. I am saving YASARA output as .pdbqt, but since it contains branch information as well so Vina was throwing error. I was suggested by YASARA support team to pass it through open babel and then save it as .pdbqt to get rid of branch information by using the appropriate flag. I did exactly according to that. But upon looking into the resultant file, it seems like it has multiple models in the file with corresponding tags, which Vina is not able to identify and hence throwing an error.[1] 

I am attaching my protein file here.[2] Can anybody please help me understand how to fix it given my few months of experience with docking simulations.

Thank you very much.

Output will be ZINC000589822496_out.pdbqt
Reading input ...

Parse error on line 3059 in file ""6w9c_+.pdbqt"": Unknown or inappropriate tag


Jatin Kashyap 
Ph.D. Student
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435 at

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