Dear Prof. Simmerling,
Thanks a lot for your help. I really appreciate it!
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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> >
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Received on Mon Oct 05 2020 - 09:00:05 PDT
