AMBER Archive (2005)

Subject: Re: AMBER: Stacking energy

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Fri Jul 01 2005 - 04:52:45 CDT

Hi Ivan,

thanks for replying. Besides the Biophys. J. that you have mentioned,

most recent are
Potential energy surface of the cytosine dimer:
MP2 complete basis set limit interaction energies,
CCSD(T) correction term, and comparison with the AMBER force field
Jurecka P, Sponer J, Hobza P
J. Phys. Chem, B 108, 5466-5471, 2004

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs
Sponer J, Jurecka P, Hobza P
J. Am. Chem. Soc. 126, 10142-10151 2004

Local conformational variations observed in B-DNA crystals do not
improve base stacking: computational analysis of base stacking
in a d(CATGGGCCCATG)(2) B <-> A intermediate crystal structure
Sponer J, Florian J, Ng HL, Sponer JE, Spackova N
Nucl. Acids. Red. 28, 4893-4902 2000

Other methods (CHARMM etc..... were tested in
J. Comput. Chem. 18, 1136-1150, 1997
Hobza et al.

Overall, amber with its RESP charges is very fortunate
and provides very good results for all kinds of neutral
complexes such as base stacking, base pairing, RNA pairing
with O2'H groups, and also for intercalators.

Jiri

-------------------------------------------------------
Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer_at_ncbr.chemi.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/labs/LSDNA/
--------------------------------------------------------

>
> Dear Angelo,
>
> have a look at this article and references therein:
>
> biophysical journal (1997) vol.73 p76-87
>
> It was both QM and MM data
>
> Hobza and sponer have worked in this area, sure they have something
> helpful
>
> Regards,
>
>
> On Fri, 1 Jul 2005, Angelo Pugliese wrote:
>
> > Hi,
> >
> > Anyone has never tried to calculate stacking energies (DNA) by AMBER? I
> > searched the archive but i did not find anything about it.
> > Thanks in advance for your help.
> >
> > Angelo Pugliese
> >
> >
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> --
> _______________________________________________
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> / Ivan Marchan Carvajal \
> | (PhD Student) |
> | |
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