From: Aravinda Munasinghe (
Date: Thu Dec 05 2019 - 09:33:27 CST

When you say a break, does it mean like none continuous backbone? or a
"kink" due to an unnatural amino acid?.
I am not familiar with your term "kink". In the case of a break due to two
chains, capping should do the job it supposed to and dynamics will be what
it supposed to (assuming you run long enough). If this is an unnatural
amino acid, and you are taking parameters from CGenFF server, based on
the penalty value you get, you should be able to determine the quality of
your parameters (assuming you are using CHARMM). If the penalties are low
(high does not mean they are bad either), they will be able to mimic the
"kink" in your protein. Without exactly knowing what is the "kink"
structure is you are talking about, I can only tell you this much.


Aravinda Munasinghe
PhD Candidate |*|* Colina Research Group
George and Josephine Butler Polymer Research Laboratory
Center for Macromolecular Science and Engineering
Department of Chemistry |*|* University of Florida
Vice President of Mayors' Council

On Thu, Dec 5, 2019 at 4:46 AM vivek nani <> wrote:

> Dear NAMD users,
> This might be a naive question.
> Let's say my molecule has a break in its structure i.e., a kink present in
> the backbone.
> Will NAMD recognize this? Can I see more fluctuations in the molecule when
> compared to a single straight backbone with no kinks?
> Or will it depend on the parameters I use? I mean that if my parameters
> recognize the kink as an improper, then I can see the difference.
> Let me know what you think.
> Thanks in advance.

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