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 Post subject: Hydrogens in vina
PostPosted: Fri Oct 03, 2014 9:26 pm 
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I know that Vina use united atom scoring fuction and merge non-polar hydrogens, i also know that polar hydrogens are used to type heavy atoms as hydrogen bond donors or acceptors. But one thing that's unclear to me: does Vina make use of polar hydrogen positions in making hydrogen bonds with ligand, or just need those cordinates only to know that those hydrogens belong to certain atom? For example i get diffrent polar hydrogens positions from ADT, Molprobity and WHAT IF when preparing protein, does Vina should give diffrent results for all this cases?


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 Post subject: Re: Hydrogens in vina
PostPosted: Thu Mar 05, 2015 8:42 pm 
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In a Vina docking, Vina tries to minimize the energy of the 'heavy_atoms' in its input model.
Vina does not try to minimize the energy of hydrogen atoms.
In fact, its only use of hydrogens is to distinguish between possible atom types to assign to the atoms bonded to the hydrogens.

Please note that the three different methods you mentioned in your post could (very likely!) result in different numbers of hydrogens for a single system. Also, probably the hydrogens added by ADT are the least reliable (compared to the other ones).


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