Re: [External Email] Constraints required for alpha helix secondary structure

From: Sandeep Dash (
Date: Fri Jul 16 2021 - 14:38:52 CDT

 Hello Diship,

I think you can try putting in constraints on the heavy atoms in the
backbone (C,N,O) during the minimization and equilibration and see how it
goes. If the secondary structure stays nearly alpha helix, then you can
proceed with an unconstrained production run. Also, apart from
net neutrality of the whole system, you may check if each of the residues
has the proper charge, as it involves the salt bridges.

On Fri, Jul 16, 2021 at 6:57 AM Diship Srivastava <> wrote:

> Hi,
> I have protein containing 28 mino acid residues. The protein has 4 leucine
> residues which forms 2 leucine zipper structures and whole protein adopting
> alpha helix config with several salt bridges between different residues. I
> started with a structure similar to this ( made by Avogadro) and I was able
> to get proper psf file. During equilibration with protein in water box
> whole protein loses its alpha helix config ( I measured the alpha helix
> content using alpha helix colvar) resulting in an open ended structure with
> less than 20% alpha helix content which was around 75 % in the initial
> structure.
> My question is what constraint do I apply to protein such that I get
> accurate description of it during equilibration and production run? Also on
> applying these constraints will it affect the PES of the system?
> Diship Srivastava
> IIT (ISM) Dhanbad
> India

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