ADL: Nitrogen atom types - NA or N?

Sargis Dallakyan sargis at
Mon Jan 7 14:02:37 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?

Hi Tomasz,

The following condition in AutoDockTools/ makes nitrogens 
hydrogen bond acceptor('N' + 'A')

                 if item.babel_type in ['N3','N2','N1']:
                     item.autodock_element = item.element + 'A'
                 elif item.babel_type in ['Nam', 'Npl', 'Ng+']:
                     if len(item.bonds)==2:
                         item.autodock_element = item.element + 'A'

Translated to English this means, nitrogen is acceptor if:
it is sp1, sp2 or sp3 nitrogen, or
it is nitrogen amide, trigonal planar or Ng+ (sp3 plus H+?), and its bonded to 2 

> "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 used the following commands after reading ind.pdb and using Ligand -> Input -> 
 >>> mv.selectFromString(atoms='N*')
 >>> mv.selection.autodock_element
['N', 'N', 'N', 'N', 'NA']
 >>> mv.selection.babel_type
['N3+', 'Nam', 'Npl', 'Nam', 'Npl']
['N1', 'N2', 'N3', 'N4', 'N5']

N5 in Indinavir is acceptor because its in the ring and bonded to 2 atoms.

Hope this helps,

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