Hi Ilyas,
I mean that ff99 for proteins has completely wrong behavior for
Gly as well as much too strong helical content for other residues.
ff99SB has (mostly) corrected these. Since so many papers have
pointed out trouble with ff99 for proteins, I would expect good reviewers
to be unwilling to accept any new work done using these parameters.
see for example
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A. and Simmerling,
C., "*Comparison of multiple Amber force fields and development of improved
protein backbone parameters*", Proteins: Structure, Function and Genetics,
3:712-725 (2006).
Carlos
On 9/7/07, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:
>
>
> > you should almost certainly not be using ff99, it is well documented
> that
> > it has very bad properties.
>
> Dear Carlos,
>
> What exactly do you mean by not using ff99?
>
> Best,
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> = Department of Chemistry - =
> = University of Rochester - =
> = Hutchison Hall, # B10 - =
> = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> = http://www.pas.rochester.edu/~yildirim/ =
> ---------------------------------------------------------------
>
>
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Received on Sun Sep 09 2007 - 06:07:33 PDT
