ADL: Some questions regartding autodock-vina: partial charges model plus ligand and receptor preparation scripts
mlists at ligand.eu
Thu Aug 27 21:11:27 PDT 2020
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
partial charges to atoms?
- same question for the ligand(s).
From the doc, I feel that Gasteiger-Marsili is the default, so I am
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:
[...]/prepare_ligand.py, [...]/prepare_receptor.py and
I wonder which one I am supposed to use: with or without the 4? and what
the meaning of this 4?
Thanks a lot,
PS: I am the kind of user who prefer to do things on the command line,
than in a GUI. Because, I like to fully automate things at some
Though, I often fire up chimera to look at (beautiful) things.
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