just to follow up and add some extra detail based on offline discussino
with Jason.. in principle the only difference is the improved dihedral
sampling in ff14SB for some of the ionizable amino acids compared to
ff99SB. These may change the ensemble sampled during the TI runs used to
calculate the reference energies. I expect, though, that since ff99SB and
ff14SB have the same nonbonded parameters that the differences in reference
energies would probably be very small.
On Mon, Nov 7, 2016 at 9:02 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> 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
>
>
> _______________________________________________
> 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 Mon Nov 07 2016 - 06:30:03 PST
