Dear Dr. Simmerling,
Thank you very much for your email,
We are interested in small fast-folding proteins which were investigated in many studies including the study described in your article, mentioned in the email, and studies at the group of DE Shaw (Lindorff-Larsen et al, 2011).
We have GPU resources and run simulations with explicit solvent. We need FFs to reproduce the protein folding process described in the literature and compare it with our results. You used ff14BSonlysc (not ff14Sb) and in the Lindorff-Larsen et al, 2011 CHARMM22* was used, though I suppose during the recent years new FFs were developed, which will more accurately describe the protein folding process.
Best regards,
Harut
-------- Forwarded message -------
From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: November 5, 2020 8:38 PM
Subject: Re: [AMBER] protein folding
how large is the protein? This is a very challenging task. Do you have
large computer facilities?
You might look at work from our lab (not very recent though) using implicit
water, and references therein for the DESRES group in explicit water.
Folding Simulations for Proteins with Diverse Topologies Are Accessible in
Days with a Physics-Based Force Field and Implicit Solvent
<
https://doi.org/10.1021/ja5032776>. Nguyen, H., Maier, J., Huang, H.,
Perrone, V., Simmerling, C., Journal of the American Chemical Society,
2014, 136 (40), 13959-13962
here is a more recent review:
Advances in free-energy-based simulations of protein folding and ligand
binding <
https://doi.org/10.1016/j.sbi.2015.12.002>. Perez, A., Morrone, J.
A., Simmerling, C. Dill, K. A., Current Opinion in Structural Biology,
2016, 36, 25–31
On Thu, Nov 5, 2020 at 11:21 AM <h_sahakyan.mb.sci.am> wrote:
> Dear Colleagues,
>
> Could you please recommend a force field for protein folding
> simulations? I found a99sb-disp which is designed for both ordered and
> disordered proteins, a crucial component in the water model. The recent
> ff19SB, also uses 4 point water moded is it a good idea to use this kind of
> force fields for protein folding simulation?
>
> What else, except the force field, should be considered, maybe
> some simulation parameters? Any recommendation is highly appreciated?
>
> Thank you in advance,
> Harut
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Received on Fri Nov 06 2020 - 06:30:04 PST
