Re: [AMBER] protein folding

From: Carlos Simmerling <>
Date: Thu, 5 Nov 2020 11:38:04 -0500

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
<>. 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 <>. 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 <> 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 Thu Nov 05 2020 - 09:00:03 PST
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