Messages

1

MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA

« on: September 16, 2020, 09:22:21 am »

Hi Xiang-jun,

Sorry for the late post. I was doing some other things and also understanding the usage of DSSR last week.

I am glad that I found out a way to apply DSSR on my trajectory without taking too much space.
The protocol is:
1. Divide the whole trajectory into let's say 1000 parts, and I would like to have 100 frames in one trajectory file. In my case, the simulation already divided the entire trajectory into small sections.
2. Use cpptraj to convert a single trajectory file into PDB file. Here, I only focus on DNA so I strip water and ions.
3. Run DSSR like

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x3dna-dssr -i=production500.pdb -o=pro500.json --more --nmr --json. Like what you suggested, I use json output here.
4. Following the manual, I used jq tool to extract information from the json file I got on step 3. E.g.

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jq '.models | .[] | .parameters.stems | .[] | {stem: .index, helical_direction: .helical_axis}’ <json file>.
5. Repeat the steps 2 to 4, and then I can retrieve helical axis information of the whole trajectory. Then I just need to concatenate them. Just make sure I only keep the useful files during the iteration so that I would not occupy too much space.

Meanwhile, I notice that, when numbering the stems, I guess the program number the stems by their residue number (from 5' to 3'), namely, the helix with smaller resid at 5' side will be numbered first... Is this correct?

Thanks so much:)

Best regards,
Moi

2

MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA

« on: September 07, 2020, 04:28:02 am »

Hi Xiang-jun,

Thank you for the detailed information! I got the license from the university last week, and then tried to install and run DSSR. Unluckily, I noticed from the manual that DSSR only support PDB and mmCIF format... while my MD trajectories are millisecond-level netCDF file... If I convert the trajectory to PDB files, it would be over 30 GB... So I cannot continue with it.

As for my motivation to use 3DNA, I started working on Holliday Junction (HJ, a kind of DNA structure with four strands forming two helices, and two of the strands are shared by the two helices) recently by computational methods. Usually, the HJ conformation can be described by directions of helices. I hope that I can use the definition in 3DNA to describe the helix vectors so that I can see how those confirmations were sampled during the simulation (I failed to deal with it with cpptraj). Also, I want to monitor the base-pair H-bond along the helices during the simulation. Although cpptraj can solve it but this work is quite tedious:(

I also read some literatures and 3DNA and Curves+ are the only methods mentioned by those authors... Frankily speaking, I don't think Curves+ has a decent manual to explain its usage... I hope I am wrong

Best regards,
Zhengyue

3

MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA

« on: September 04, 2020, 05:15:43 am »

Hi Xiang-Jun,

Thank you for your detailed reply! Considering the microsecond-level AMBER trajectories and the situation of 3DNA, I finally asked the license of DSSR. I am still waiting for their response:)

Hopefully, DSSR can solve my problem, I would like to try it and then have feedback here.

Thanks again!

Best regards,
Moi

4

MD simulations / Failed Downloading MD Ruby Scripts of 3DNA

« on: September 02, 2020, 04:31:37 am »

Hello!

I am new to 3DNA and would like to use 3DNA for my MD trajectory analysis. So far, I have installed the standard 3DNA v2.4 and know that MD Ruby scripts and do_x3dna are two options for me.

However, I got a problem on entering  http://3dna.rutgers.edu:8080/data/x3dna_md_v0.1.tar.gz website. The browser said "this site cannot be reached". I further tested 3dna.rutgers.edu website and it still failed. Is it a problem of the server?

I am really expecting to try 3DNA and looking forward to the reply:)

Best regards,
Moi