it looks like ff14SB is available on that link, it is called amber14SB
there.
it does include terminal capping groups such as ACE. I believe CT2
corresponds to NHE in amber (amidated), but you'll want to check it and
make sure it is what you want.
On Sat, Oct 10, 2020 at 2:49 PM Asaf Farhi <asaf.farhi.gmail.com> wrote:
> Dear Prof. Simmerling,
>
> Thanks again for your help.
> I will be happy to hear your recommendation about the best way to use
> ff14SB in Gromacs.
> There is the link with a few options
> http://www.gromacs.org/Downloads/User_contributions/Force_fields
>
> In addition, I wanted to ask if there is a force field for the terminal
> residues e.g., ACE and CT2.
>
> Thank you for your help,
> Best regards,
> Asaf
>
>
>
> On Mon, Oct 5, 2020 at 11:37 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > see my comments inserted below
> >
> > On Mon, Oct 5, 2020 at 11:31 AM Asaf Farhi <asaf.farhi.gmail.com> wrote:
> >
> > > Dear all,
> > >
> > > My name is Asaf and I'm a postdoc at Creol, UCF.
> > >
> > > I would be happy to consult with you regarding the choice of force
> field
> > > for proteins.
> > > I have read in the manual that the recommended force field for proteins
> > is
> > > ff14SB.
> > >
> > > I have a few questions and I would really appreciate your help:
> > > 1. What does SB stand for?
> > >
> >
> > SB stands for Stony Brook, my home institution. All of the protein models
> > from my lab are indicated with the "SB"
> >
> >
> > > 2. Can the CMAP parameters be changed (manually) in free energy
> > > calculations with Gromacs?
> > >
> >
> > I don't know how Gromacs handles CMAPs, it may be better to ask Gromacs
> > developers. Note that ff14SB does not include CMAPs, so this may not
> > matter. ff19SB includes CMAPs, and ot my knowledge this is not yet
> > implemented in Gromacs since we use different CMAPs for different amino
> > acids.
> >
> >
> > > 3. What is the recommended force field without CMAP?
> > >
> >
> > ff14SB does not use CMAPs
> >
> >
> > > 4. Are Amber99 or Amber99sb*-ILDN recommended?
> > >
> >
> > Amber99 (really should be called ff99) is not recommended, it is very old
> > and should no longer be used.
> > ff99SB*-ILDN is more recent, but my recommendation would be to use ff14SB
> > instead. Of course others may have good experience with ff99SB*-ILDN as
> > well. It included some backbone and sidechain updates to our ff99SB
> model,
> > but ff14SB has a more extensive refitting of side chain parameters (in
> > addition to a small backbone adjustment).
> >
> >
> > > Thank you for your help,
> > > Best regards,
> > > Asaf
> > > _______________________________________________
> > > 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
> >
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Oct 11 2020 - 04:30:02 PDT
