Topics

1

MD simulations / How to analyze helical parameters of DNA with unnatural bases

« on: September 18, 2017, 09:31:20 am »

Dear Mr Lu,
  Recently, we are trying to use the 3DNA to analyze helical parameters in our DNA MD simulations. However, base pairs DX:DA / DY:DA / DZ:DA can’t be recoganized when I used “find_pair”. Notably, the unrecoganized base-pair (named DX, DY, DZ, DA) are not typical purine or pyrimidine. How can I analysis the conformation parameters with 3DNA in a such case. 
  The pdb files of DX, DY, DZ, DA and a frame of MD simulations are given in the attachment . Thank you very much!

Best wishes!

Xiehuang Sheng

2

General discussions (Q&As) / how to analyze base-stacking interactions with 3dna

« on: May 10, 2016, 09:35:45 pm »

Dear Xiang-jun,

      You said that base-stacking interaction could be analyzed with 3dna software (http://x3dna.org/citations/quantification-of-base-stacking-interactions-using-overlap-area). Could you show me how to do it, or which files?

      Best Wishes!

Xiehuang Sheng

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Shandong Normal University, Shandong, China

3

MD simulations / How to Analysis the Conformation Parameters of Unnatural base in MD

« on: October 17, 2015, 04:10:43 am »

Dear Mr Lu,

Recently, we performed 200 ns of molecular dynamics (MD) simulations on some DNA sequences containing unnatural nucleobase pairs using Amber 14, a total of 100000 frames. Now, we try to illustrate the dynamicvariation of DNA structure in the whole process by analyzing DNA structural parameters (such as slide, roll, twist,etc) of all frames.

Amber has a built-command analyzing some of unnatural bases such as 8OG, <nastruct naout nastruct.dat resrange 274-305 resmap 8OG:G>, but it comes to error “N0 N1” when I use this command.

Now my question is that if 3DNA can analyze DNA parameters of all frames by setting some parameters. If possible, please recommend somereading material. Thank you very much!

Best wishes!
Xiehuang Sheng