AMBER Archive (2003)

Subject: Re: AMBER: Mg2+ parameters for RNA usage

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Wed Dec 10 2003 - 13:32:57 CST

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_at_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
> ibmc-cnrs
> 15 rue ren? descartes
> f-67084 strasbourg cedex
> france
>
> tel: (33) 388 41 70 49
> mob: (33) 616 98 55 07
> fax: (33) 388 60 22 18
>
> e-mail: p.auffinger_at_ibmc.u-strasbg.fr
> http://www-ibmc.u-strasbg.fr/upr9002/westhof/biblio_pascal.html
> ________________________________________________________________
>
>
> -----------------------------------------------------------------------
> 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