Messages

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) / Re: how to analyze base-stacking interactions with 3dna

« on: May 11, 2016, 08:28:14 am »

 Dear Xiangjun,
         
Thanks a lot for you reply. I am understand how to do it .

Best Wishes!

xeihuang sheng
----------------------

Shandong Normal University, Shandong,China

3

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

-----------------
Shandong Normal University, Shandong, China

4

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

« on: November 07, 2015, 02:41:44 am »

Alternatively, with sufficient programing skills, you could divide your snapshots into smaller chunks (say 100 pieces). You can then run 'x3dna_ensemble analyze' on each in parallel. In the end, you need to combine the result from each run together. This is just a general idea for you to think about and play with.

Dear Mr Lu,

It's a good idea. thank you very much!

Best wishes!

Xiehuang Sheng

5

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

« on: November 06, 2015, 09:45:19 pm »

Dear Mr Lu,
   
     We can use x3dna_ensemble to analyze the MD trajectories. But we are faced with a new problem.  The MD analysis is time-consuming for large system which contains 100,000 snapshot. it will cost our over 24 hours. I wonder to know wheher x3dna_ensemble can work in parallel, such as x3dna_ensemble.MPI. Thank you very much!

Best wishes!

Xiehuang Sheng

6

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

« on: October 22, 2015, 12:16:03 am »

Dear Mr Lu
       I really appreciate your help in modifying the software script for my case. I can do it by myself, Now.  The procedure as following,
    a, releasing all snapshots from the trajectories of Amber MD simulations
    b, building pbfile.dat with pair_find
    c, using x3dna_ensemble to analyze all the snapshots.        x3dna_ensemble analyze -b pbfile.dat -p 'XX/XX_*.pdb' -o ensemble.out
    d, extracting all the parametes from the result.       x3dna_ensemble extract -f ensemble.out -a
    By the way, I will study the protein-DNA interaction in the next project. Which software should I use, thank you.

Best Wishes!
Xiehuang Sheng

7

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

« on: October 20, 2015, 06:05:11 am »

Dear Mr Lu
     Thank you for your elaborate explanatin. I will try it in following days. By the way, whether should I study both sortwares, 3DNA and DSSr. thank you very much!
      Best wishes!

Sheng Xiehuang

8

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

« on: October 18, 2015, 02:25:02 am »

Dear Mr Lu
       Thank you for your kindly reply.
       The unnatural base-pair  (named DX, DY) are not typical purine or pyrimidine.  The structure of DX， DY and a frame of DNA structure are in the attachment (have stripped out water and Na+).   How can I analysis the conformation parameters with 3DNA in a such case. thank you very much!

BEST wishes!
Sheng Xiehuang

9

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