AMBER Archive (2006)

Subject: Re: AMBER: alpha helix preference problem

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu May 25 2006 - 20:35:10 CDT

ff99 itself won't be changing. there are modified forms of ff99 that do
have improved secondary structure balance- the one from my lab is called
ff99SB in amber9. A manuscript is in review and I'd be happy to give you
a preprint if you are interested.

ff03 also has improved properties but the charge model is not
compatible with all of the parameters developed for ff94/ff99, such
as the nucleic acids parameters or many small molecule parameters
that people have developed over the years. ff99SB will work fine with these.
carlos

harianto wrote:

>Hi, Amber users,
>
>Has the problem of the alpha helix over-preference solved for
>the ff99 of amber 8 version?
>
>I did "diff" with parm99 of amber 7.
>The only difference was atom type "N3".
>What is this change?
>
>
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