Just a follow up to Carlos'...
I would say that presently SIRAH 2.0 isn't the best choice for folding/unfolding experiments...
Indeed, we showed that depending on the system "some success" can be obtained, like in the case of the short hairpin in TRP cage [
https://doi.org/10.1021/acs.jctc.9b00006], the extended conformations in IDPs [
https://doi.org/10.1021/acs.jctc.0c00948] and small peptides [
https://doi.org/10.1016/j.csbj.2021.02.014]... but alpha-helix can't be folded (e.g. [AAQAA]3) [
https://doi.org/10.1021/acs.jctc.9b00006]...
Hence, I doubt about the SIRAH performance on folding complex domains... most probably it won't work...
I have some hints to improve both the SIRAH force field for proteins and its implicit/explicit solvent simulation, but this is work in progress...
Best regards,
MatÃas Machado
----- Mensaje original -----
De: "Carlos Simmerling" <carlos.simmerling.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Domingo, 21 de Marzo 2021 11:00:45
Asunto: Re: [AMBER] SIRAH CG Protein with Implicit Solvent
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]
>
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 21 2021 - 08:00:01 PDT
