AMBER Archive (2007)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed Aug 22 2007 - 11:08:29 CDT


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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