Recent Posts

41

MD simulations / Re: Do I need gromacs to use dnaMD for simulations?

« Last post by xiangjun on May 16, 2025, 10:00:09 am »

Thanks for the x3DNA-DSSR software which works wonderfully for single PDBs.

Thanks for using DSSR and for posting your questions on the 3DNA Forum. As for the analysis of an ensemble, please see the DSSR manual , especially Section: "3.13 The --nmr option":

The DSSR --nmr (or --md) option automates the analysis of an ensemble, such as NMR structures in the PDB or snapshots from MD simulations. The input coordinates file must be in either the classic PDB format where each model is delineated by MODEL/ENDMDL tags, or the mmCIF format where each ATOM/HETATM record has an associated model number.
...
The --json option makes it easy to parse the output of multiple models pragmatically. In addition to NMR structures, trajectories from MD simulations can also be processed. Popular MD packages (AMBER, GROMACS, CHARMM, etc.) all have their own specialized binary formats for trajectories. By design, DSSR does not work on these binary files. They must be converted to the standard PDB or mmCIF format to be analyzed by DSSR. The combination of --nmr and --json makes DSSR directly accessible to the MD community.

I have some MD simulations I would like to analyze with dnaMD. I ran them with Amber but converted them to GROMACS .xtc + .pdb files for analysis.

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

I am not a practitioner of MD simulations. Questions related to dnaMD are best answered by its developer: hopefully @rkumar will chime in. See the thread Update of do_x3dna package, which can be used with files generated by GROMACS.

PS. I am also lacking the link to download the 3DNA from the forum for some reason, my forum view is similar to unregistered users.

There have been too many spam registrations nowadays, so I must stay continuously vigilant to keep the Forum clean. You should now see the download link. Sorry for the inconvenience.

Best regards,

Xiang-Jun

42

MD simulations / Do I need gromacs to use dnaMD for simulations?

« Last post by piia600 on May 16, 2025, 05:50:16 am »

Hi all,

Thanks for the x3DNA-DSSR software which works wonderfully for single PDBs.

I have some MD simulations I would like to analyze with dnaMD. I ran them with Amber but converted them to GROMACS .xtc + .pdb files for analysis.

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

PS. I am also lacking the link to download the 3DNA from the forum for some reason, my forum view is similar to unregistered users.

43

RNA structures (DSSR) / Re: Building G-quadruplexes

« Last post by xiangjun on May 05, 2025, 10:57:00 am »

Hi shr,

Following the discussion in the previous thread on "Rebuilding circular Z-DNA", as quoted below:

In addition to Z-DNA, I also work on other non-canonical DNA structures, particularly G-quadruplexes (G4s). I’m developing a method to construct ideal G-quadruplex models from sequence data by first arranging guanine bases into tetrads, then building in the backbone and loop regions.

I am glad to hear about your work on G-quadruplexes. Actually, I have recently revised the G4 module in DSSR, fixed existing bugs, and added new features. The g4.x3dna.org website has undergone a complete overhaul, enabling users to upload their own structures for dynamic G4 analysis. Additionally, the DSSR-G4DB database is being actively updated on a weekly basis as new PDB entries are added. See the four blog posts comparing DSSR with other related analysis tools on G-quadruplexes: ASC-G4, Webba da Silva nomenclature, ElTetrado and related tools, and CIIS-GQ.

Moveover, I am also interested in modeling G-quadruplexes, taking G-tetrad as the building block. There are quite a few other threads in DSSR I'd like to pursue further in the future. I'd certainly like to hear more about your approach on modeling G-quadruplex.

I dug into the code of DSSR for modeling G-quadruplexes, and found the following experimental (and undocumented) features. DSSR can model G-quadruplexes using G-tetrad as the building block, and allows users to specify the number of G-tetrads and twist angle (among other things). See below for two examples: one with 3 layers of G-tetrads and 0 degrees of twist angle, and other with 6 layers and twist=36, respectively.

Best regards,

Xiang-Jun

44

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by xiangjun on May 05, 2025, 10:21:04 am »

Hi Di,

Are you still interested in the topic of modeling circular Z-DNA? I'm planning for a new release of DSSR (v2.5.3) which includes new features for modeling nucleic acid structures. It would be great to hear your feedback on how it works in your specific case.

I take user questions seriously as they provide valuable opportunities to enhance the software. Each piece of user feedback helps me think in ways I might not have considered otherwise. By analyzing feedback and integrating suggestions, DSSR becomes more robust and user-friendly. At the same time, I consistently adopt a systematic approach when introducing new features, ensuring they are thoroughly tested and reliable while addressing users' concerns.

Best regards,

Xiang-Jun

45

RNA structures (DSSR) / Re: Contour of dsDNA/dsRNA

« Last post by tengxj12345 on May 01, 2025, 12:28:19 pm »

Thanks for your detailed explanation. I will check it out.

46

RNA structures (DSSR) / Re: Contour of dsDNA/dsRNA

« Last post by xiangjun on April 30, 2025, 11:38:47 pm »

Thanks for your clarification. The two attachments are very helpful. Now I can use the following 3DNA commands to reproduce the results:

Code: Bash

1. find_pair coor_7972.pdb | analyze

The output file "coor_7972.out" has exactly the same parameter as the attached file "summary.txt".

Now back to your question:

it seems quite strange. The helix doesn't follow the structure of my DNA well. Is there anything wrong, or there are other output can better represent the contour?

The "strange" behavior you are observing is due to the sensitivity of helical parameters to local structural variations. There is nothing wrong as far as 3DNA goes. To verify this, you could try the following two things:

* Build a perfectly regular fiber RNA duplex model using the command below, and repeat your procedure. You should see a straight helix as expected. For example, see Figures 1 and 9 of the 2003 3DNA paper.

Code: Bash

1. fiber -seq=AAAAAAAAAA -rna fiber-RNA-A10.pdb
2. # or better yet, using DSSR v2.5.2
3. x3dna-dssr fiber --rna-duplex --seq=A10 -o=dssr-fiber-RNA-A10.pdb

* With the parameters from 3DNA analyze output (bp_step.par or bp_helical.par), you can run rebuild to generate a structure. The RMSD between the original structure and the rebuilt one should be close to 0 for base + C1' atoms. If you analyze the rebuilt structure, you should get virtually identical helical parameters as for the original structure. The analyze/rebuild reversibility is one of the core features of 3DNA and DSSR, originating from the SCHNAaP/SCHNArP pair of programs based the CEHS algorithm.

Hope this helps! Basically, what you are observing is the expected behavior of 3DNA.

That being said, for visualization purposes, one might want to smooth the local variations using Bezier curves or similar methods.

Best regards,

Xiang-Jun

47

RNA structures (DSSR) / Re: Contour of dsDNA/dsRNA

« Last post by tengxj12345 on April 30, 2025, 10:44:44 pm »

Sure. I attached my pdb file. I uploaded to the webserver and generated summary.txt.

The last section of the file (Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step) was then used to draw the centroids. I can get the same results bu running it on my local computer (find_pair and analyze).

48

RNA structures (DSSR) / Re: Contour of dsDNA/dsRNA

« Last post by xiangjun on April 30, 2025, 10:31:11 pm »

Hi Xiaojing,

Thanks for posting on the 3DNA Forum. Could you please provide details about how you generated the contour plot for dsDNA/dsRNA you attached? These would include the PDB or mmCIF coordinates file, and the exact DSSR/3DNA commands you used. The goal is reproducibility and to help others understand the process better.

Best regards,

Xiang-Jun

49

RNA structures (DSSR) / Contour of dsDNA/dsRNA

« Last post by tengxj12345 on April 30, 2025, 09:48:25 pm »

Hello,

I tried to get the contour of dsDNA/dsRNA structures. I think the output from helical section should be it. When I plot the positions of local helical axis along with my pdb, it seems quite strange. The helix doesn't follow the structure of my DNA well. Is there anything wrong, or there are other output can better represent the contour?

Thanks,
Xiaojing Teng

50

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by xiangjun on April 30, 2025, 08:40:24 am »

Hi Di,

How about the attached results? Does it meet your expectations?

Best regards,

Xiang-Jun