AMBER Archive (2007)

Subject: Re: AMBER: Force field for RNA with U-turn motif

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Wed Aug 22 2007 - 11:33:46 CDT

Hi Jenk,

I would use both, but see no physical reason to mix them,
i.e., one nucleotide this ff, another that ff.
Comparison of both ff would be interesting.
I would use parmbsc0 as the standard when starting
a new project right now.

U-turn types of RNA structures are likely to show backbone dynamics,
at least we have seen this in amber simulations.
Jana Sefcikova et al.
The genomic HDV ribozyme utilizes a previously unnoticed
U-turn motif to accomplish fast site-specific catalysis
Nucleic Acids Res., March 2007; 35: 1933 - 1946
Though we did not reach any convincing conclusion.

Best wishes, Jiri

[ Charset ISO-8859-1 unsupported, converting... ]
> Thanks Vlad.
>
> Any more comments? What about the new parmBSC0 force field?
> or should I use a combination of both? For instance, can I just use parm99 parameters for the alpha torsion angle following U33 in the anticodon loop and use parmBSC0 parameters for the rest of the RNA?
>
>
> regards,
>
> jenk
>
> Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote: Hi Jenk,
>
> I believe amber ff99 is what you want ...
>
> Greets
> vlad
>
> Cenk Andac wrote:
>
> > Dear Amber community,
> >
> > I was wondering if anyone could recommend a suitable force field for
> > the anticodon loop region of t-RNA showing a U-turn motif in its
> > X-Ray structure..
> >
> > my best regards,
> >
> > jenk
> >
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>
>
>
> --
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