AMBER Archive (2005)

Subject: Re: AMBER: Stacking energy

From: Angelo Pugliese (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Fri Jul 01 2005 - 05:42:28 CDT

Hi Ivan and Jiri,

Thanks for your help.
I am just reading the article :

J. Phys. Chem, B 108, 5466-5471, 2004

Jiri, could explain me how do u used AMBER to calculate the energies ? I mean how
do u extract from the energies just the values for one specific base pair....or may
be your system is just one base pair and nothing more?

Thanks

Angelo

Jiri Sponer wrote:

> 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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> > --
> > _______________________________________________
> > / \
> > / Ivan Marchan Carvajal \
> > | (PhD Student) |
> > | |
> > | Institut de Recerca Biomedica de Barcelona |
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