it really depends on what is meant by "fix the alpha helix better".
Certainly it was much better with ff99SB. Also maybe the reviewer needs to
be reminded that water model also has a significant impact on results, as
we discuss in the ff19SB paper (and others have reported too).
On Thu, May 28, 2020 at 9:56 AM Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> Wasn't this a known problem with ff94, that was already addressed in
> ff99SB?
>
> --
> Gustavo Seabra
> ________________________________
> From: Seketoulie Keretsu <sekekeretsu.gmail.com>
> Sent: Thursday, May 28, 2020 8:51:12 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Amber99SB force field
>
> Dear AMBER User,
>
> During a protein interaction study, we were asked by reviewer to change
> force field from Amber99SB to Charmm27 as the Charmm27 is likely to fix the
> alpha helix better. From our literature, review we were of the impression
> that both forcefields are fairly reasonable in representing protein
> (non-membrane proteins) particularly in protein folding. Am i missing
> something?
>
> Would appreciate if you can give your opinion or reference to related work.
>
> Thank you.
>
> Sincerely,
> Seke
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Received on Thu May 28 2020 - 07:30:02 PDT
