ADL: Some questions regartding autodock-vina: partial charges model plus ligand and receptor preparation scripts

Diogo Martins diogo.stmart at gmail.com
Fri Aug 28 10:14:45 PDT 2020


Hello,

Vina and Autodock4 are different programs and different scoring functions.
Vina, unlike autodock4, does not use electrostatics or partial charges - it
will ignore such values. I use the scripts with the "4", or "42" if
available, I think they indicate the version of autodock they are
designed to work with.

Best regards,


On Thu, 27 Aug 2020 at 23:14, Francois Berenger <mlists at ligand.eu> wrote:

> Dear list,
>
> Recently, I started to play with autodock-vina, in the probably
> vain quest of teaching myself some protein-ligand docking (my academic
> background completely lacks biochemistry, and my chemistry knowledge
> is only scarce and learned "on-the-job").
>
> But, I find the protein-ligand docking topic interesting/intriguing,
> and I like the autodock-vina paper and I _love_ the fact that the
> software is open-source.
>
> So, here are my questions:
> - when preparing the receptor protein, is there a recommended model to
> assign
>    partial charges to atoms?
> - same question for the ligand(s).
>
>  From the doc, I feel that Gasteiger-Marsili is the default, so I am
> wondering
> if this is really what vina was using during its scientific validation,
> and hence would be the recommended partial-charges model. While, I would
> prefer to use MMFF94 for the ligands, for example, and whatever chimera
> recommends for the target protein.
>
> In my chimera installation, there are scripts like:
> chimera-1.14/lib/python2.7/site-packages/AutoDockTools/Utilities24/prepare_ligand4.py,
>
> [...]/prepare_ligand.py, [...]/prepare_receptor.py and
> [...]/prepare_receptor4.py.
>
> I wonder which one I am supposed to use: with or without the 4? and what
> is
> the meaning of this 4?
>
> Thanks a lot,
> Francois.
>
> PS: I am the kind of user who prefer to do things on the command line,
> rather
>      than in a GUI. Because, I like to fully automate things at some
> point.
>      Though, I often fire up chimera to look at (beautiful) things.
>
>
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>
>


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