The Molecular Graphics Laboratory Forum

Autodock vina Question
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Author:  shivakumarpd [ Tue Jul 08, 2014 3:49 pm ]
Post subject:  Autodock vina Question

I need some help running Autodock vina. I watched this video on you tube ( and followed all the instructions. However, I get some error message when I run the docking.
My question is should all the program file (Autodock vina), protein and ligand files be in the same drive while running the docking.


Author:  Ruth Huey [ Thu Mar 05, 2015 8:56 pm ]
Post subject:  Re: Autodock vina Question

The simplest format is to put the Autodock vina executable file along with the required input files in the same folder (or directory). The usual input files include: protein.pdbqt, ligand.pdbqt and config.txt.

Author:  devika [ Wed Aug 17, 2016 7:43 am ]
Post subject:  Re: Autodock vina Question

I am using Autodock Vina for docking.
I have 622 small molecules for virtual screening. Can I use Vina?
I tried with command prompt "vina --config conf.txt"
it shows that
Parse error on line 1 in file "ligand.pdbqt": Unexpected multi-MODEL input. Use "vina_split" first?

Thus on a search I came to know the shell script from the tutorial, saved the script in the same folder, used the command in prompt "vina --config conf.txt --ligand $f --out ${b}/out.pdbqt"
but I got error
"Command line parse error: too many positional options".
Kindly direct me how can I rectify this problem?
Thanks in advance.

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