Re: secondary structure restraints in coarse grain

From: Jesper Sørensen (
Date: Tue Jul 24 2012 - 16:35:37 CDT

Dear Eun,

It sounds like you are looking for an elastic network model, not to restrain the secondary structure, but the tertiary structure. You should look at the MARTINI CG website for that and also ask in their forums.


On Jul 24, 2012, at 1:37 PM, Aron Broom wrote:

> The MARTINI CG model used by NAMD is already secondary structure constrained. That is, you give it the secondary structure of your protein, and the dihedrals for the CG beads are locked into that kind of secondary structure. But maybe you want something more than that?
> On Tue, Jul 24, 2012 at 2:35 PM, Eun Kim <> wrote:
> Hello,
> I would greatly appreciate if anyone could help me on finding restraining the secondary structure of CG model.
> this constraints would be not on the space, but constraints on extra bonds.
> I find that there is a plugin/scripts for allatom models which generates extra bonds to be constrained, but not for the CG one.
> Any help please!
> Thanks in advance
> Eun
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo

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