Dear Carlos and Jason,
Many thanks for your replies. I am quite keen to use ff14SB instead of
ff99SB.
I might try to titrate the model compounds, at least for my peace of mind.
Many thanks,
Eric
On 4 November 2016 at 19:52, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> 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
>
--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Mon Nov 07 2016 - 04:00:03 PST
