We haven't had good luck with SIRAH and GB for that type of simulation. we
are working on adapting our GB model but are a ways off still. SIRAH was
developed to use their WAT4 explicit water.
On Sat, Mar 20, 2021, 1:09 PM Leung, Jeremy <JML230.pitt.edu> wrote:
> Hi Amber Developers and Users,
>
> My lab and I are trying to simulate a protein unfolding/folding using the
> SIRAH force field in implicit solvent and were wondering if we could get
> some help on which implicit solvent model to use.
>
> The Amber user guide mentions that only igb=1 (with DNA) is supported. We
> did some tests with igb=8 (which we previously used with other all-atom
> proteins) and we noticed that, at the minimum, the protein did not blow up
> (though did unfold a little at early stages). I was wondering if the
> comment in the user guide was due to the fact it was not extensively tested
> on other implicit solvent models? Or were there other issues that happened
> during testing? If so, are there any suggestions/recommendations regarding
> that?
>
> Thanks in advance,
>
> Jeremy Leung
>
> --
> Jeremy M. G. Leung
> Predoctoral Fellow, Chemistry
> Graduate Student Researcher, Chemistry (Chong Lab)
> University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
> jml230.pitt.edu<mailto:jml230.pitt.edu> | [He, Him, His]
>
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Received on Sun Mar 21 2021 - 07:30:02 PDT
