AMBER Archive (2005)

Subject: Re: AMBER: Stacking energy

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Fri Jul 01 2005 - 09:01:24 CDT

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
> > > >
> > > >
> > > > This message has been checked for viruses but the contents of an attachment
> > > > may still contain software viruses, which could damage your computer system:
> > > > you are advised to perform your own checks. Email communications with the
> > > > University of Nottingham may be monitored as permitted by UK legislation.
> > > >
> > > > -----------------------------------------------------------------------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber_at_scripps.edu
> > > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > > >
> > >
> > > --
> > > _______________________________________________
> > > / \
> > > / Ivan Marchan Carvajal \
> > > | (PhD Student) |
> > > | |
> > > | Institut de Recerca Biomedica de Barcelona |
> > > | Parc Cientific de Barcelona |
> > > | Molecular Modelling & Bionformatics Group |
> > > | http://mmb.pcb.ub.es |
> > > | |
> > > | C/ Josep Samitier 1-5 08028 Barcelona |
> > > | Tel: +34.93.403.71.55 Fax: +34.93.403.71.57 |
> > > | |
> > > | E-mail: ivan_at_mmb.pcb.ub.es |
> > > | theochem_at_hotmail.com |
> > > | Website: http://mmb.pcb.ub.es/~ivan |
> > > \ /
> > > \_________________________________________________/
> > >
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
> This message has been checked for viruses but the contents of an attachment
> may still contain software viruses, which could damage your computer system:
> you are advised to perform your own checks. Email communications with the
> University of Nottingham may be monitored as permitted by UK legislation.
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu