Re: structure changing

From: Aron Broom (
Date: Thu Oct 11 2012 - 06:33:53 CDT

In most common forcefields (e.g. CHARMM, AMBER) all ranges of secondary
structure are possible, so there is no reason why such a transition
shouldn't be possible.

On Thu, Oct 11, 2012 at 12:51 AM, <> wrote:

> Dear NAMD Users
> I compute pulling the protein which has helix structures.
> When I pull the protein, some helix structures break and change to loop
> structures.
> In NewCartoon, it looks like that heavy coil changes thin cord.
> Instead, I wonder if loop structures changes helix structures in NAMD
> calculation.
> Is the loop structures able to change the helix structures in NAMD
> calculation?
> If this is a poor question, I'm sorry.
> I'm beginner of NAMD and English.
> Ishii Kai

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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