On Fri, Nov 4, 2016 at 11:08 AM, Eric Lang <eric.lang.bristol.ac.uk> wrote:
> Hello,
>
> I am going to run some pH-REMD simulations in explicit solvent of an
> helical protein.
>
> I understand that CpHMD, and by extension pH-REMD, are parametrised with
> ff10 (equivalent to the ff99SB force field used in the original Mongan
> paper).
>
> However, since my structure is composed solely of alpha helices, I am
> concerned about the tendency of ff99SB (and ff10) to under-stabilise alpha
> helices and thus model an unrealistic partial unfolding of the helices.
>
> I understand that ff14SB has some updated torsion terms for Phi and Psi
> angles to improve the accuracy of alpha helix simulations.
>
> Could I therefore use ff14SB instead of ff10 to run my CpHMD without
> problems or would this require to re-calculate the model compounds pKa,
> update the parameters for the ionisable residues, and perhaps other things?
>
​Short and simple answer is, "I don't know". It would be easy to check,
though -- titrate the model compounds and see if the pKas come out about
right. If they do, then the force field is fine.
That said, I suspect you will be able to use ff14SB without needing to
change the reference energies. Formally this is a false statement, but if
the necessary change is negligible (i.e., within the range of uncertainty
of the current reference energy) -- as I suspect it is -- then it is
practically true.
HTH,
Jason
--
Jason M. Swails
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Received on Fri Nov 04 2016 - 13:00:02 PDT
