Re: [AMBER] SIRAH CG Protein with Implicit Solvent from Leung, Jeremy on 2021-03-22 (Amber Archive Mar 2021)

From: Leung, Jeremy <JML230.pitt.edu>
Date: Mon, 22 Mar 2021 15:59:09 +0000

Thank you so much for the advice. We'll definitely rethink over our options.

-- JL
--
Jeremy M. G. Leung
Predoctoral Fellow, Chemistry
Graduate Student Researcher, Chemistry
University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml230.pitt.edu | [He, Him, His]

> On 21 Mar 2021, at 10:55 AM, Matias Machado <mmachado.pasteur.edu.uy> wrote:
>
> 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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1021%2Facs.jctc.9b00006&data=04%7C01%7CJML230%40pitt.edu%7Ce9d6c20fe0c54146cb1d08d8ec7984af%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637519353969560676%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gF6FJJmf7qW5Re65DFFkQNyz6EDOouMzUh0yeoMqUwY%3D&reserved=0], the extended conformations in IDPs [https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1021%2Facs.jctc.0c00948&data=04%7C01%7CJML230%40pitt.edu%7Ce9d6c20fe0c54146cb1d08d8ec7984af%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637519353969560676%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=WFyf3Lg0YfjJ5L8ic9509CHtVTbQkNnOOeQ6Xfx51%2BY%3D&reserved=0] and small peptides [https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.csbj.2021.02.014&data=04%7C01%7CJML230%40pitt.edu%7Ce9d6c20fe0c54146cb1d08d8ec7984af%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637519353969560676%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=r6rq8kj%2FpzHWDBQredIp7sohWSeYWfTaaHvDBaPmXvE%3D&reserved=0]... but alpha-helix can't be folded (e.g. [AAQAA]3) [https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1021%2Facs.jctc.9b00006&data=04%7C01%7CJML230%40pitt.edu%7Ce9d6c20fe0c54146cb1d08d8ec7984af%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637519353969560676%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gF6FJJmf7qW5Re65DFFkQNyz6EDOouMzUh0yeoMqUwY%3D&reserved=0]...
>
> 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,
>
> Matías 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]
>>
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Received on Mon Mar 22 2021 - 09:00:02 PDT