From: vivek nani (
Date: Thu Dec 05 2019 - 10:17:12 CST

It is not a break in the molecule, kink is nothing but a part of the
molecule coming out of the plane.

On Thu, 5 Dec 2019 at 21:03, Aravinda Munasinghe <>

> Hi,
> 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.
> Best,
> 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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