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PostPosted: Wed May 20, 2015 6:57 pm 
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Joined: Wed Jun 23, 2010 10:25 am
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Dear all,

Maybe I am asking a stupid question but ...
Vina refers to the X_score[1] atom typing scheme and
in this X_score atom classification, "H-bond acceptors"
refer to "sp2 or sp hybridized nitrogen atoms". Why are
sp3 hybridized nitrogen atoms (such
as those in simple R-NH2 amines) prevented
from being able to form hydrogen bonds in Vina
as hydrogen-bond acceptors ?

Thanks in advance.
Ric

[1] Journal of Computer-Aided Molecular Design, 16: 11–26, 2002.


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PostPosted: Wed Jul 01, 2015 3:41 pm 
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This snippet from page 2 of the vina paper: "AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading" explains why:

"The hydrogen atoms are not considered explicitly, other than for atom typing, and are omitted from Eq.1" which is the conformation dependent part of the scoring function..."


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