The reviewer is incorrect. Both ff99SB and charmm27 (which is really charmm22+ nucleic acids and cmap in gromacs) have alpha-helical bias (depending on the peptide). Generally, ff99SB is well behaved for well folded proteins (there are a few exceptions in the literature) and is fairly standard. If you do need to re-run to satisfy the reviewer, moving to ff14SB or ff19SB (I would actually stick to ff14SB as it has a longer track record and likely you can find additional benchmarks to respond to reviewer comments with) I think would be advisable.
Additionally, charmm27 is actually quite old, (charmm36m is now out) so you may want to include that point somewhere in your response.
-Micholas
-----Original Message-----
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, May 28, 2020 9:16 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [EXTERNAL] Re: [AMBER] Amber99SB force field
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 It has been replaced by ff14SB, and more recently by ff19SB.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 - 12:00:02 PDT
