ADL: Nitrogen atom types - NA or N?

Tomek Wlodarski tomek.wlodarski at
Sat Jan 5 14:21:12 PST 2008


I am new in this field so sorry if my question is to basic.
I am using AutoDock4 with ADT and almost in every case when I try to make
pdbqt file for my ligand all nitrogens are in N autodock atom type - so they
can not be acceptor in hydrogen bond - but i do not understand why....??
My question is when I can have NA and when N nitrogen type - when nitrogen
can't be a hydrogen bond acceptor?
All oxygen are in OA form, and this is ok for me - why the same situation is
not in nitrogen case?
In Tutorial it is used Indinavir as ligand and then:

"Nitrogens which can accept hydrogen-bonds are assigned AutoDock
type 'NA' while those which cannot are assigned 'N'. In
indinavir, the AutoDock type of atom N5 in the heterocycle
is 'NA' while the other nitrogens are assigned 'N'."
Why only heterocycle?
I would be very grateful for help


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