Hi Pascal,
this is interesting, I did not know about
that we have multiple parameter sets.
We possibly could somehow compare them or exchange
experience.
We did a comparison of "AMBER" Mg2+ vs. QM though
not yet an in-depth one (essentially upon a referee request).
Gresh N. et al, J. Phys. Chem. B 107, 2003, 8669
For those interested there are additional QM studies
cited there that show the missing terms.
(The total amount of non-additivity in the first
ligand shell of Mg2+ is on a huge scale of 100 kcal/mol,
although fortunately there is a substantial degree
of compensation of errors when moving from
QM to nonpolarisable MM).
Another big problem for Mg2+ simulations is how much
can one rely on the initial X-ray Mg2+ positions? I think
Pascal addressed this issue few times before.
I found an amazing RNA X-ray paper Ennifar et al. Nucl. Acids Res.
31, 2003, 2671. This analysis goes far beyond
what is usual in X-ray studies, to my opinion.
Best wishes, Jiri
-------------------------------------------------------
Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer.ncbr.chemi.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/labs/LSDNA/
Senior Wellcome Trust International Research Fellow for Biomedical Science
--------------------------------------------------------
[ Charset ISO-8859-1 unsupported, converting... ]
> Dear Vlad,
>
> Mg2+ parameters are to be found in the parm91 and parm99 AMBER force-fields
> parm91: 1.10 0.10
> parm99: 0.7926 0.8947
> We use the first set of parameters which seems to provide correct results
> (although polarization and charge transfer effects are not taken into
> account as mentionned by Jiri), see Chem Biol 2003 10 551
>
> Pascal
>
>
> > Dear ambers,
> > Could somebody indicate me some literature where I can find
> > parameters for Mg2+ used in RNA simulations?
> > Thank you very much
> > vlad
>
>
> ________________________
> pascal auffinger
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>
> e-mail: p.auffinger.ibmc.u-strasbg.fr
> http://www-ibmc.u-strasbg.fr/upr9002/westhof/biblio_pascal.html
> ________________________________________________________________
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Received on Wed Jan 14 2004 - 15:53:07 PST
