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Questions and answers > MD simulations
Failed Downloading MD Ruby Scripts of 3DNA
Moi Zhang:
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
xiangjun:
Hi Moi,
--- Quote ---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.
--- End quote ---
Thanks for your interest in using 3DNA and for posting on the 3DNA Forum. The Ruby scripts distributed with 3DNA v2.4 may be appropriate for the analysis of an NMR ensemble in the PDB or short snapshot of MD trajectory. Check $X3DNA/bin/x3dna_ensemble script and $X3DNA/examples/ensemble.
"do_x3dna" is a third-party tool based on 3DNA. As far as I know, the "do_x3dna" project is no longer supported. Search the 3DNA Forum may give you some info.
--- Quote ---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?
--- End quote ---
The 3dna.rutgers.edu server is hosted by Rutgers University. You may get any information on it from Dr. Wilma Olson. I have nothing more to offer on this matter.
You may try DSSR with the --nmr and --json options for MD analysis. As noted recently in the announcement post "DSSR 2.0 is licensed by Columbia University", "DSSR 2.0 supersedes 3DNA 2.4, which is still maintained but no additional features other than bug fixes are scheduled."
Best regards,
Xiang-Jun
Moi Zhang:
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
xiangjun:
Hi Moi,
--- Quote ---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:)
--- End quote ---
Yes, DSSR 2.0 is the way to go. See the overview PDF.
Please let me know if you still do not hear back from CTV by early next week.
--- Quote ---Hopefully, DSSR can solve my problem, I would like to try it and then have feedback here.
--- End quote ---
I am curious to know why do you want to use 3DNA/DSSR for the analysis of MD trajectories? Aren't there already dedicated tools (e.g., AMBER: CPPTRAJ) that *should* do the job, conveniently? In other words, what are still missing in those ready-to-use tools? I may be interested in extending MD analysis features in DSSR 2.0, ONLY IF justified by real-world applications.
Best regards,
Xiang-Jun
Moi Zhang:
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
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
