Eric, h
Please test it and get back to us with your answers. We have used ff14SB
constant pH for about 6 months now, including testing, and we have not
yet seen a difference with ff99SB.
adrian
On 11/7/16 4:29 AM, Eric Lang wrote:
> 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
>>
>
>
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Nov 07 2016 - 06:30:03 PST
