ADL: Hydrogens in vina

Bartosz Pająk therealcosta at gmail.com
Mon Oct 20 06:58:10 PDT 2014


Ok, thank you very much for clearing that up. So as i see there is no sense
in trying to build good hydrogen bonds network in receptor because vina
take into account only presence of hydrogens.

2014-10-20 14:22 GMT+02:00 Bartosz Pająk <therealcosta at gmail.com>:

> Dear Vina users,
> 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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