AMBER Archive (2006)

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

From: Vlad Cojocaru (
Date: Fri Apr 14 2006 - 04:57:33 CDT

Dear David, amber users,

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?

If I may, as a short comment on this, I believe that it is important to
be able to use the same ff for both proteins and nucleic acids (perhaps
membranes also) as they do coexist and many simulations involve
complexes ... Therefore it is not very helpful if features proven to
improve the ff quality added on the course of ff development are not
transferred to newer versions .

If for objective reasons, such features cannot be transferred to newer
versions of the ff, it would be very helpful if this will be clearly
specified in the Amber manual..

Best wishes

David A. Case wrote:

>On Thu, Apr 13, 2006, Vlad Cojocaru wrote:
>>my understanding of the Amber ffs is that a newer version does retain
>>the attributes of an older version (unless proven faulty) so ff99 should
>>retain the torsion angle parameters involving the glycosidic torsion
>>from ff98.
>Tom Cheatham should weigh in here with the correct pointers; but I am pretty
>sure that ff99 does not include the changed nucleic acid parameters of ff98.
>Be sure to read at least the nucleic acid force field review cited at the top
>of the Amber web page.
>The AMBER Mail Reflector
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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