ADL: Hydrogens in vina

Bartosz Pająk therealcosta at gmail.com
Mon Oct 20 06:08:13 PDT 2014


So how Vina knows where hydrogen bonds are if it dont look at
hydrogens directionality?
It just assumes that whenever hydrogen donor and acceptor are close enough
there will be hydrogen bond?

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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