Disagreements with experiment really are a result of the *combination *of
solute force field and the solvent model, and other simulation protocols.
In this case, I think it's very difficult to say that a modern force field
overestimates helical conformations without knowing which water model is
being used, and even then it is hard to know which component is at fault.
For example, there is literature now suggesting that TIP3P explicit water
overly favors compact conformations (such as helices), and unraveling the
water model errors from protein force field errors is very difficult. Our
current evidence suggests that ff14SB actually understabilizes helices
somewhat, and TIP3P overstablizes them, leading to some (imperfect)
cancellation of error with this combination. Using ff14SB with a different
water model would lead to different results (helices could be either too
stable or not stable enough, depending on which water model you choose).
We have quite a bit of discussion on this topic in our ff19SB manuscript
that is available on ChemRxiv.
https://doi.org/10.26434/chemrxiv.8279681.v1
Carlos
On Tue, Sep 3, 2019 at 1:49 PM Lod King <lodking407.gmail.com> wrote:
> Hi Amber
>
> I was told that ff14SB seems to overestimate the helical conformation?
> I wonder if there are any papers bring up this issue?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 03 2019 - 11:30:02 PDT
