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 - 05:31:24 CDT

Hi Vlad,

     I would tell that all available pair-additive force fields derived
     from Cornell et al have similar applicability and
     it is not straightforward to tell which of the variants
     is better. Our experience is that if one version works
     then the other works too, and vice versa.

     Molecular dynamics simulations of guanine quadruplex loops:
     Advances and force field limitations
     Fadrna E, Spackova N, Stefl R, Koca J, Cheatham TE, Sponer J
     BIOPHYS J 87, 227-242, 2004

     The main advantage of the AMBER force field is the use of
     ESP charges, thus it works excellently for stacking,
     H-bonding, including RNA interactions (RNA base pairs).
     Backbone is more difficult since it has complicated electronic
     structure and the charges not necessarily work in all
     its substates equally well, in addition it is a polarisable
     anion. We have recently completed a test (ca 3 microseconds
     in total) for a wide range of functional RNA molecules with
     difficult topologies and the results
     are quite optimistic. The results are summarized in
     some papers published recently or comming out right now.

     Of course, description of ions is less accurate especially
     for divalents (I would advice everyone to not include
     divalents unless really necessary based on very clear
     high resolution x-ray data).
     Caution is needed with chlorines, polarisable species
     difficult to treat with pair additive ff.

     But may be really Tom should comment on it.

     Jiri

[ Charset ISO-8859-1 unsupported, converting... ]
> 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
> vlad
>
>
> 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.
> >
> >....dac
> >-----------------------------------------------------------------------
> >The AMBER Mail Reflector
> >To post, send mail to amber_at_scripps.edu
> >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
> >
>
> --
> 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
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu