From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Fri Jul 16 2021 - 11:08:33 CDT
Dear Diship,
Did you neutralize the whole system electrostatically?
---
,Best
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:shekaari_at_email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.google.com/citations?hl=en&user=LDzbXB4AAAAJ&view_op=list_works&sortby=pubdate__;!!DZ3fjg!tLapbJpVcCmriGdRUlfwNjwDLXw3knztLNwJHTlfU4gIgFv5vpJXXmFZEwcZjnxBgQ$ ]
From: "Diship Srivastava" <dishipsrivastava_at_gmail.com>
To: "namd-l" <namd-l_at_ks.uiuc.edu>
Sent: Friday, July 16, 2021 3:21:56 PM
Subject: namd-l: Constraints required for alpha helix secondary structure
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
JRF
IIT (ISM) Dhanbad
India
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