Re: [AMBER] continuous DNA

From: Thomas C. Bishop <bishop.latech.edu>
Date: Thu, 9 May 2019 14:33:40 -0500

I extended bonds across the periodic boundaries for a short simulation
of 147bp of dna in 2005.

T.C. Bishop. Conformation and Dynamics of Nucleosomal and Free DNA. J.
Biol. Struc. Dyn. 22(6): 673-686, 2005.

Structurally this is same as circular DNA so tleaps topology can handle it
However as noted the unit cell should be 10.5*n basepair long to make
sure the DNA is not over/underwoound
so 21 bp works pretty well. So 10.5*3.4 *n is about the size of the cell

Interestingly since it's circular dLk = dTw + dWr
if dLK = 0 then dTW = - dWr
(did I get those in all correct order?)
If the protein bends the DNA then it has to also be coupled w/ twisting
DNA for this particular setup.

Be careful about how you setup AND scale the periodic cell as this will
introduce tension in the DNA. I would not scale along the "z-axis" (long
axis of DNA).

I'm very interested in how this works out!
Tom



On 5/9/19 1:53 PM, Ilyas Yildirim wrote:
> The only way you can build such a system is by creating a special case where you align the DNA in z-axis, and play with the coordinates so that the image boxes overlaps with the ends of the DNA mimicing an infinitely long DNA. The first and last basepairs of the images should keep the system stable. We did a similar work on an RNA system.
>
>
> Yildirim, I., Chakraborty, D., Disney, M. D., Wales, D. J., and Schatz, G. C., "Computational Investigation of RNA CUG repeats responsible for Myotonic Dystrophy 1", J. Chem. Theory Comput. 11, 49434958, 2015
>
> https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5b00728
>
>
> Best,
>
>
> Ilyas Yildirim, Ph.D.
> ---------------------------------------------------------
> = Assistant Professor =
> = Department of Chemistry & Biochemistry =
> = Florida Atlantic University =
> = 5353 Parkside Drive, Building MC17, Jupiter, FL 33458 =
> =
> = Phone: +1(561)799-8325 | E-mail: iyildirim.fau.edu =
> ---------------------------------------------------------
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> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
> ---------------------------------------------------------
>
> ________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: Thursday, May 9, 2019 1:44:04 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] continuous DNA
>
> On Thu, May 09, 2019, Qinghua Liao wrote:
>> I am running simulations of protein-DNA systems, as the DNA sequences
>> are quite long,
>> I am wondering how I can set up a continuous DNA along one axial
>> directions.
> I'm not sure exactly what you mean. Amber doesn't allow covalent bonds
> between molecules in different unit cells. So: you can't create an
> "inifinite" helix making use of periodic boundary conditions.
>
> But I'm not at all sure if this is what you meant by your question.
>
> ...dac
>
>
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-- 
  ***********************************
         Thomas C. Bishop
Hazel Stewart Garner Associate Professor
        Chemistry & Physics
         Tel: 318-257-5209
         Fax: 318-257-3823
        www2.latech.edu/~bishop
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Received on Thu May 09 2019 - 13:00:02 PDT
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