Re: [AMBER] Several alpha-helices stitched together - how would you stress-test it with MD?

From: Carlos Simmerling <>
Date: Tue, 28 Jan 2020 05:52:49 -0500

The possibility in md depends on strongly on the size and your
computational resources. How long is it? Note that a single long helix
requires a much larger periodic box than the same peptide length when it
forms a helical bundle.

On Tue, Jan 28, 2020, 5:48 AM Homeo Morphism <>

> We are trying to assemble a long alpha-helix by stitching together known
> but shorter alpha-helices.
> We've gone through the appropriate literature on the subject before
> committing to individual fragments and the secondary structure prediction
> tools are saying there's a chance our final structure will end up folding
> as a long alpha-helix indeed.
> Is there any way we can also buttress these results with MD simulations? I
> can think of two obvious things:
> 1) just waiting for it to unfold from an already folded state;
> 2) watching how it will be folding from a completely unfolded state or a
> random coil.
> Any other suggestions?
> Thank you.
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Received on Tue Jan 28 2020 - 03:00:02 PST
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