AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 14 2006 - 10:27:52 CDT

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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