the ff99SB force field has *many thousands* of citations. If the reviewer
presents a specific peer reviewed article that states that what you are
trying to do is a known problem for ff99SB, then it might be reasonable. In
my opinion it is not appropriate for a reviewer to simply state that you
should use a different force field without significant justification. I
cannot say much more though because you don't give details on what the
reviewer meant by "fix the helix".
Having said that, ff99SB is indeed an older model. It has been replaced by
ff14SB, and more recently by ff19SB. I would suggest using one of those
since they are updates to ff99SB.
On Thu, May 28, 2020 at 8:51 AM Seketoulie Keretsu <sekekeretsu.gmail.com>
wrote:
> 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 - 06:30:02 PDT
