AMBER Archive (2005)

Subject: Re: AMBER: Stacking energy

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Fri Jul 01 2005 - 10:00:03 CDT

Hi Angelo,
This in principle could be applied, though I doubt one
can easily subtract "stacking" component of that,
decompositions are tricky.
So, be careful, computers never hesitate to give numbers,
not all numbers make a sense.

Jiri

> Hi Jiri,
>
> I am performing MD in explicit solvent on a DNA-PNA complex.
> Yes, I should include the hydration free energies and even the entropies. What do you
> think if I use MM-PBSA and Normal Mode Calculations to iclude these contributions?
>
> Angelo
>
>
>
> Jiri Sponer wrote:
>
> > For reference calculations, we use our geometries of bases/base pairs.
> > Van der Waals term is taken directly from Cornell, charges can either
> > be recalculated via (R)ESP, or just taken from Cornell and neutralized at
> > the site where the glycosidic bond was cut.
> >
> > When taking MD structures, you need to use just an appropriate
> > part of the force field energy, just take care that your subsystems
> > entering the calcs are strictly neutral, otherwise you get
> > "charge charge" effects that are large in vacuo.
> >
> > I do not know the purpose of your calcs.
> > Note that all these energies are gas phase energies and cannot
> > be compared with "stability" of stacking in nucleic acids,
> > which is affected by tons of other effects such as solvent
> > screening specifically modulated by a shape of a given NA
> > form, other hyudration effects, entropy etc.
> >
> > 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/
> > --------------------------------------------------------
> >
> > > 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 |
> > > > > | Parc Cientific de Barcelona |
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