Re: Constraints required for alpha helix secondary structure

From: Ashkan Shekaari (
Date: Fri Jul 16 2021 - 11:08:33 CDT

Dear Diship,

Did you neutralize the whole system electrostatically?

Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ ] [;!!DZ3fjg!tLapbJpVcCmriGdRUlfwNjwDLXw3knztLNwJHTlfU4gIgFv5vpJXXmFZEwcZjnxBgQ$ ]

From: "Diship Srivastava" <>
To: "namd-l" <>
Sent: Friday, July 16, 2021 3:21:56 PM
Subject: namd-l: Constraints required for alpha helix secondary structure

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

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