Thamk you, Viktor -
That's great help!
Joseph
On Wed, 1 Mar 2006, Viktor Hornak wrote:
> Joseph Nachman wrote:
>
> >Can yuo recommend any of the papers discussing the problems of parm96?
> >
> >
> >>I would also add my opinion that unless you have a very good reason,
> >>you should not be using parm96. It has some serious problems
> >>that have been documented in the literature.
> >>
> >>
>
> Here is a few papers dealing with ff96 (I am sure there's more), in
> particular check Ono et al that specifically discusses the propensity of
> ff96 to form extended structures:
>
> Kamiya N, Higo J, Nakamura H. Conformational transition states of a
> beta-hairpin peptide between the ordered and disordered conformations in
> explicit water. Protein Science 2002;11(10):2297-2307.
>
> Higo J, Ito N, Kuroda M, Ono S, Nakajima N, Nakamura H. Energy landscape
> of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn,
> beta-hairpin, and other disordered conformations. Protein Science
> 2001;10(6):1160-1171.
>
> Ono S, Nakajima N, Higo J, Nakamura H. Peptide free-energy profile is
> strongly dependent on the force field: Comparison of C96 and AMBER95. J
> Comput Chem 2000;21(9):748-762.
>
> Wang L, Duan Y, Shortle R, Imperiali B, Kollman PA. Study of the
> stability and unfolding mechanism of BBA1 by molecular dynamics
> simulations at different temperatures. Protein Science 1999;8(6):1292-1304.
>
> Cheers,
> -Viktor
>
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--
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Joseph Nachman Department of Biochemistry
nachman.hera.med.utoronto.ca University of Toronto
Medical Sciences Building
tel: +1 416 978-5510 Toronto, Ontario M5S 1A8
fax: +1 416 978-8548 Canada
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Received on Sun Mar 05 2006 - 06:10:14 PST
