ADL: autodock Digest, Vol 107, Issue 4

Koes, David dkoes at pitt.edu
Sat Jul 6 13:27:45 PDT 2013


You can try smina: http://smina.sf.net

smina is a fork of Autodock Vina that is optimized for scoring and minimization.  It doesn't support zip files, but you can pass any multi-molecule file format that is supported by openbabel.  For example:
smina -r rec.pdbqt -l ligands.sdf -o output.sdf --autobox_ligand crystal_ligand.mol2

This will dock all the ligands in ligands.sdf against rec.pdbqt using a box defined around crystal_ligand.mol2.

If you want, you can also specify your own custom scoring function, although in my experience the default Vina scoring function performs the best (despite my efforts to improve upon it).

David Koes

Research Assistant Professor
Computational & Systems Biology
University of Pittsburgh

http://www.pitt.edu/~dkoes/

On Jul 6, 2013, at 3:00 PM, autodock-request at scripps.edu wrote:

> Hello,
> 
> 
> 
> I am a new user of Vina. I have a library of ligands in zip format in which
> 
> I have thousands of ligands in pdbqt format. How can I include this library
> 
> in configuration file for Autodock Vina. I am using windows platform for
> 
> operation.
> 
> 
> 
> Thanks,
> 
> 
> 
> Pooja Makkar, PhD







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