AMBER Archive (2006)

Subject: Re: AMBER: Which one is the best force field for DNA?

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Fri Apr 14 2006 - 11:59:00 CDT

Hi Dave,

for RNA and G-DNA, I would tell we see no differences, all
versions have the same performance, the G-DNA loops being
the trouble, but with all versions. RNA is pretty safe so far.
I think tom has the same experience.

Jiri

> On Fri, Apr 14, 2006, Vlad Cojocaru wrote:
> >
> > Well, I did read sometime ago Tom's review, maybe I missed (or I forgot)
> > some of the information there so I'll read it again ...So, I didnt know
> > that ff99 (thus also ff03) doses not include the ff98 changes. Is there
> > a particular reason why those changes were not included in newer versions?
>
> The "short" answer is that it is not clear that the changes made in ff98
> are actually improvements. For example, one the the largest recent set of
> simulations (the so-called "ABC" group working on duplex DNA), chose ff94
> as the best force field for that purpose. [See Biophys. J. 87:3799, 2004 and
> 89:3721, 2005.] I believe that many people would have similar sentiments for
> RNA. Others on the list may wish to chime in here.
>
> .....dac
>
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