Dear Prof. Simmerling,
Great, thanks a lot for your help. I really appreciate it. I chose one of
these force fields (few with ff14SB).
Best regards,
Asaf
On Sun, Oct 11, 2020 at 7:27 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > > > _______________________________________________
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Received on Fri Oct 16 2020 - 15:30:02 PDT
