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 Post subject: Autodock vina Question
PostPosted: Tue Jul 08, 2014 3:49 pm 
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Hello,
I need some help running Autodock vina. I watched this video on you tube (http://www.youtube.com/watch?v=-GVZP0X0Tg8) 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.

Regards,
Shivakumar


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PostPosted: Thu Mar 05, 2015 8:56 pm 
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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.


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PostPosted: Wed Aug 17, 2016 7:43 am 
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Hello,
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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