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

Francois Berenger mlists at
Thu Aug 27 21:11:27 PDT 2020

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 
   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:
[...]/, [...]/ 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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