Dear Vlad:
We use for RNA I guess radius 0.7926, well depth 0.8947,
and I think these are taken from Ross&Hardin JACS 1994
paper. See for example Reblova et al Biophys. J. 84, 2003,
3564-3582. There are other papers with Mg2+, Tsui&Case JPC B
105, 11314, Hermann et al Eur. Biophys. J. 27, 1998, 153 etc etc.
Nevertheless, whatever the parameters are, the force
field remains far from reality due to a neglect of
major polarization and charge transfer effects.
Sampling of Mg hexahydrates is very poor at the ns scale.
So, unless really specifically needed it is rather better to avoid
any divalent ions in a simulation.
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
--------------------------------------------------------
> Dear ambers,
> Could somebody indicate me some literature where I can find
> parameters for Mg2+ used in RNA simulations?
> Thank you very much
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail: Vlad.Cojocaru.mpi-bpc.mpg.de
> home tel: ++49-551-9963204
>
>
>
>
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Received on Wed Jan 14 2004 - 15:53:06 PST
