Re: AMBER: nonplanarity of NH2 groups

From: Jiri Sponer <>
Date: Thu, 7 Dec 2006 18:37:52 +0100 (MET)

Dear Laura,

you can find a correct electronic structure description
of DNA/RNA aminogroups in

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
Author(s): Sponer J, Leszczynski J, Hobza P
Source: BIOPOLYMERS 61 (1): 3-31 2001


Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations
Author(s): Hobza P, Sponer J
Source: CHEMICAL REVIEWS 99 (11): 3247-3276 NOV 1999

and some "biological" role of noplanar RNA amino groups for example in:

Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs
Author(s): Sponer J, Mokdad A, Sponer JE, Spackova N, Leszczynski J, Leontis NB
Source: JOURNAL OF MOLECULAR BIOLOGY 330 (5): 967-978 JUL 25 2003

The NH2 has a flexible electronic structure, which in isolation
is partially sp2-sp3 pyramid, and in real environment is
"manipulated" by the environment. Primary H-bonds (including
hydration) tend to shift to sp2. So for most but not
all interactions in DNA and RNA sp2 is relevant.

Standard parameters of AMBER assume sp2 hybridization,
(which for most interactions is OK)
but they still allow some nonplanarity of the hydrogens,
albeit smaller than would be optimal for "real" nucleobase.
(not a true pyramidalization)
So 10 deg dihedral nonplarity is I think acceptable,
but I suggest to check whether the amino group does not
have a reason to seek to be out of plane.
Amino groups can be involved in out-of-plane H-bonds
as well as in amino-acceptor H-bonds.

Note that "accurate" ff would be difficult since
it would have to flexibly respond by its sp2-sp3 balance
to the environment and create a lone pair above the nitrogen.
It is nothing that could be easily done by dihedral parameters,
for example.

Best wishes, Jiri

Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133

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> Dear all,
> My question is about NH2 non-planarity. If I carry out AMBER minimizations on nucleic acids, what kind of non-planarities can I expect? For example, is it normal to get a value of 10 degrees for the N3-C4-N4-H41 dihedral in cytosine? I know the AMBER force feild cannot model this type of non-planarities, but I want to know if deviations from planarity of 10-15 degrees are normal.
> I hope you can help me.
> Thanks,
> Laura
> ---------------------------------
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Received on Fri Dec 08 2006 - 16:23:17 PST
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