Thanks a lot.
On Tue, Sep 3, 2019 at 11:17 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 03 2019 - 12:00:02 PDT
