Messages

1

FAQs / Re: Where to download x3DNA

« on: April 27, 2026, 10:24:39 am »

Hi Changdong,

Thank you for the follow-up.

I would like to clarify that the licensing for DSSR is managed by Columbia Technology Ventures (CTVs). While DSSR has a large global community with hundreds of academic users, licenses are generally not issued to institutions in certain countries due to institutional compliance and administrative policies. Unfortunately, this means that even if an academic request is submitted, it may be restricted based on the location of the host institution.

However, you can still access DSSR through the following options:

• DSSR v1.9.10-2020apr23: This version is available for download directly from the 3DNA Forum. It corresponds to the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" (2020) published in Nucleic Acids Research.
• wDSSR: You can use the recently released web interface for DSSR at https://web.x3dna-dssr.org/.
  

I appreciate your interest in the software and your understanding of these constraints.

Best regards,

Xiang-Jun

2

FAQs / Re: Where to download x3DNA

« on: April 24, 2026, 07:22:52 am »

Hi Changdong,

Thanks for your interest in 3DNA/DSSR. Your question has been addressed in another thread: License requested.

Please don’t hesitate to ask questions on the forum, but kindly avoid posting the same query in multiple threads to keep the discussion organized.

Best regards,

Xiang-Jun

3

RNA structures (DSSR) / Re: License requested

« on: April 24, 2026, 07:13:13 am »

Hi Changdong,

Thanks for reaching out. You should now be able to see the Download link at the very top of the forum.

Due to a high volume of spam, I have implemented a filter for registered users. Although your account was created in 2018, it remained in a "Pending" category because you had not yet posted on the 3DNA Forum. Once a user's first post is approved, the Download link becomes visible automatically.

Best regards,

Xiang-Jun

4

Bug reports / Re: Missing DNA bases with negative residue number

« on: April 14, 2026, 02:12:50 pm »

Hi Mihir,

Great catch! I have successfully reproduced the issue. The bug is due to a parsing error within the wDSSR web interface. As shown below, the core DSSR engine itself handles negative residue numbering without any issues.

Execute the following command to see the enumeration:

Code: [Select]

x3dna-dssr mutate -i=9GBV.pdb --enum
An excerpt of the output is as follows:

# For each entry to be mutated, remove the leading #, and add to=base

# To mutate A.A9 to G in PDB entry 1ehz (tRNA):
#          #  chain=A name=A num=9  #9  A.A9
#       --->  chain=A name=A num=9 to=G

# To mutate B.DT19 to DC in PDB entry 355d (B-DNA):
#          #  chain=B name=DT num=19  #19  B.DT19, pairedNt=A.DA6
#       --->  chain=B name=DT num=19 to=DC

# Empty or comment (starting with #) lines are ignored.

#  chain=E name=DT num=-37  #1  E.DT-37, pairedNt=F.DA80
#  chain=E name=DG num=-36  #2  E.DG-36, pairedNt=F.DC79
#  chain=E name=DC num=-35  #3  E.DC-35, pairedNt=F.DG78
#  chain=E name=DC num=-34  #4  E.DC-34, pairedNt=F.DG77
#  chain=E name=DA num=-33  #5  E.DA-33, pairedNt=F.DT76
#  chain=E name=DT num=-32  #6  E.DT-32, pairedNt=F.DA75
#  chain=E name=DC num=-31  #7  E.DC-31, pairedNt=F.DG74
#  chain=E name=DA num=-30  #8  E.DA-30, pairedNt=F.DT73
#  chain=E name=DG num=-29  #9  E.DG-29, pairedNt=F.DC72
#  chain=E name=DA num=-28  #10  E.DA-28, pairedNt=F.DT71
#  chain=E name=DA num=-27  #11  E.DA-27, pairedNt=F.DT70
#  chain=E name=DA num=-26  #12  E.DA-26, pairedNt=F.DT69
#  chain=E name=DA num=-25  #13  E.DA-25, pairedNt=F.DT68
#  chain=E name=DC num=-24  #14  E.DC-24, pairedNt=F.DG67
......

We will resolve this wDSSR error shortly. In the meantime, please continue using the tool and report any further issues you encounter.

If it is an option for your workflow, I recommend installing the standalone version of DSSR on your computer and using the command-line interface directly.

Best regards,

Xiang-Jun

5

Bug reports / Re: Missing DNA bases with negative residue number

« on: April 14, 2026, 11:34:06 am »

Hi,

Thank you for using our tools and for reaching out on the forum.

To help us investigate this further, could you please provide a step-by-step description of your workflow? Specifically, please include the exact commands or options you used so that we can reproduce the issue on our end. This will help us determine why the residues with negative numbers are not being displayed as expected.

Best regards,

Xiang-Jun

6

General discussions (Q&As) / Re: Approach for building G-quadruplex models with 3'-3' and 5'-5'polarity inversion

« on: April 06, 2026, 02:02:29 pm »

Hi muha,

Thanks for posting on the Forum, and sorry for the late reply.

I understand your aim to build a unimolecular G-quadruplex model with alternating 5'-3', 3'-3', 3'-5', and 5'-5' linkages. DSSR does not have a built-in option for building such models, and I am not aware of any other software that can do this. In my understanding, this would require a combination of DSSR and a 3D manual editing tool to adjust the polarity of the linkages.

As far as analysis is concerned, DSSR should be able to identify G-tetrads, and may take each tract as broken chains. We need specific examples to show how DSSR should behave in these cases. I will consider modifying DSSR to handle these cases if feasible.

Best regards,

Xiang-Jun

7

FAQs / Re: Where to download x3DNA

« on: April 01, 2026, 03:03:00 pm »

Hi Luca,

Thanks for your interest in 3DNA. You should now be able to see the download page on the 3DNA Forum.

Best regards,

Xiang-Jun

8

Site announcements / Staff Associate II (Computational Structural Biology) at Columbia University

« on: April 01, 2026, 01:36:23 pm »

The X3DNA-DSSR resource is at the forefront of structural bioinformatics, developing advanced tools for analyzing and modeling nucleic acid structures. We are seeking a highly motivated Staff Associate II to join our team and contribute to our next-generation analysis and visualization engine.

To see our resource in action, please visit wDSSR, our new web interface for dissecting and modeling 3D nucleic acid structures: https://web.x3dna-dssr.org/.

We are looking for a candidate with a strong scientific background in structural biology or bioinformatics and a desire to contribute to peer-reviewed publications through community-driven data analysis. We value individuals who are eager to learn, adapt to new technical challenges, and support the global research community.

For the full job description and to submit your application, please visit the official Columbia University posting:
https://apply.interfolio.com/183705

9

Site announcements / Announcing wDSSR: The Next-Generation Web Interface to X3DNA-DSSR

« on: March 17, 2026, 05:30:52 pm »

Dear 3DNA/DSSR Community,

We are thrilled to announce the official launch of wDSSR (https://web.x3dna-dssr.org/), the powerful new web interface to the X3DNA-DSSR analytical engine.

Developed by Drs. Shuxiang Li and Xiang-Jun Lu and supported by NIH grant R24GM153869, wDSSR represents a major leap forward from our highly popular 2019 Web 3DNA 2.0 framework. While Web 3DNA 2.0 has faithfully served the community for the analysis, visualization, and modeling of 3D nucleic acid structures, wDSSR was built from the ground up to take full advantage of modern web technologies and the latest DSSR backend capabilities.

A Modern, Streamlined Scientific Workflow
We have completely overhauled the user interface to provide a clean, intuitive, and task-driven experience. The core modeling and analysis tools are now seamlessly organized into a logical, single-word scientific workflow: Analyze, Rebuild, Model, Circularize, Mutate, Assemble, and Visualize.

Spotlight Feature: The "Assemble" Module
One of the most exciting upgrades is the newly renamed Assemble tab (formerly "Composite"). This advanced composite model builder allows you to effortlessly construct complex, higher-order models by linking any combination of nucleic acid duplexes or protein-DNA/RNA complexes. You can quickly connect up to six distinct target structures, ranging from simple linked A-DNA and B-DNA duplexes to large, protein-decorated structural assemblies.

Immediate Global Adoption
Although wDSSR has just launched, we are incredibly humbled to share that it is already seeing rapid worldwide adoption! According to recent network infrastructure data, the new interface is actively being used by researchers across North America, South America, Europe, and Asia. Within just a few days, we have recorded active sessions from prestigious institutions around the globe, including:

• The Weizmann Institute of Science in Israel
• Katholieke Universiteit Leuven in Belgium
• Queen's University in Canada
• Universidad Nacional Autonoma de Mexico (UNAM) in Mexico
• Emory University and the Wadsworth Centers Laboratories and Research in the United States
• Jawaharlal Nehru University and the China Education and Research Network in Asia

How to Cite
While a dedicated paper for wDSSR is currently in preparation, researchers should cite the server using its URL (https://web.x3dna-dssr.org/) alongside the 2019 Web 3DNA 2.0 paper and the foundational 2015 DSSR paper. Full details and funding acknowledgements can be found on our newly consolidated About page.

We invite you all to try out the new wDSSR platform! As always, your feedback is invaluable to us, and we encourage you to share your thoughts, questions, and structural models via the newly updated Questions & Feedback link in the wDSSR footer.

Happy modeling!

10

FAQs / Re: Where to download x3DNA

« on: February 19, 2026, 09:29:26 am »

Hi Luca,

You should now have access to the Downloads section. To prevent spam, we manually monitor and verify all new registrations. This is a one-time process; now that you are verified, you can download the 3DNA software and post questions here in the forum.

Best regards,

Xiang-Jun

11

General discussions (Q&As) / MOVED: Looking for a way to speed up do_x3dna process.

« on: February 15, 2026, 11:16:07 pm »

This topic has been moved to MD simulations.

http://forum.x3dna.org/index.php?topic=1060.0

12

MD simulations / Re: Looking for a way to speed up do_x3dna process.

« on: February 15, 2026, 11:15:42 pm »

Hi Karn,

Thanks for posting on the 3DNA Forum. Since you are using do_x3dna, Dr. Kumar (@rkumar) is the best person to answer your question. I've move this thread to MD simulations section which is more relevant to MD simulations. Hopefully, he will chime in soon.

Best regards,

Xiang-Jun

13

MD simulations / Re: Clarification on how DNA radius is computed from 3DNA/DSSR

« on: February 03, 2026, 09:25:43 am »

Hi Mamta,

Thanks for using 3DNA and for posting your question on the 3DNA Forum.

3DNA performs a least-squares fit of linear global helical axes using equivalent C1' and RN9/YN1 atom pairs along each strand of a DNA duplex. It then calculates mean and deviation of helix radius based on P, O4', and C1' atoms. Of course, the linear global helical axes is only meaningful when the DNA duplex is not strongly distorted. You may also want to check Curves+ for deriving curvilinear helical axes.

Using 355d as an example, running 3DNA as below:

find_pair 355d.pdb | analyze

You will get an output file 355d.out, which contains the following content:

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.30(0.52)
Helix:    -0.1269   -0.2753   -0.9530
HETATM 9998  XS    X X 999      17.536  25.713  25.665
HETATM 9999  XE    X X 999      12.911  15.677  -9.080
Average and standard deviation of helix radius:
      P: 9.42(0.82), O4': 6.37(0.85),  C1': 5.85(0.86)

You can extract the two HETATM lines into the original PDB file, and draw a line between them to visualize the global helical axis (in PyMOL, for example).

The underling algorithm is based on the NewHelix/FreeHelix program, and you can check the implementation details in the 3DNA source code.

Hope this helps.

Best regards,

Xiang-Jun

14

FAQs / Re: Where to download x3DNA

« on: January 11, 2026, 08:01:28 pm »

Hi,

You should now be able to see the Download section. Note that the current version of DSSR is distributed by the Columbia Technology Ventures (CTV).


Thanks for your interested in 3DNA/DSSR. If you have any questions, please do not hesitate to post them on the Forum.

Best regards,

Xiang-Jun

15

General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA

« on: December 30, 2025, 12:37:31 pm »

Hi

I'd like to run some DNA simulations employing 3D-DART and I faced this same issue in my Linux. Could I receive one x3DNA version 2.15 to test in my DNA sequence?

In the current context, I assume you are trying to download x3DNA v1.5 together with 3D-DART.

I have added links to the Downloads section for this specific version and its corresponding user manual. Once logged in, you should find the Downloads section at the top of the 3DNA Forum. Please let us know if you encounter any issues.

Best regards,

Xiang-Jun

16

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: December 24, 2025, 10:58:53 am »

As a follow-up to my previous response, DSSR v2.7.1-2025dec22 checks the stereochemistry of sugar. For each L-sugar, the JSON output will contain the key/value: "is_L_sugar": true in the nts object.

For example, running the following DSSR command on PDB entry 4WB2:

Code: [Select]

x3dna-dssr -i=4wb2.pdb --json | jq '.nts[] | {nt_id, is_L_sugar}'
will generate the following JSON output (excerpt):

Code: [Select]

......
{
  "nt_id": "D.0G35",
  "is_L_sugar": true
}
{
  "nt_id": "D.0C36",
  "is_L_sugar": true
}
......

In version v2.7.0-2025dec09, DSSR checks for flipped base pairs relative to the backbone direction. In this aspect, the L-form shares the same topology as Z-DNA, and both are left-handed helices. In version v2.7.1-2025dec22, DSSR takes into account the stereochemistry of the sugar to clearly distinguish between L and Z-form DNAs based on their L- and D-sugar configurations.

In this process, DSSR has been enhanced in multiple areas like classification and rebuilding by incorporating the L-form into a comprehensive framework. I highly value user feedback because it provides new insights that I might otherwise overlook. Once I fully grasp an issue, it often leads to an improved version of DSSR.

Xiang-Jun

17

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: December 08, 2025, 11:36:31 pm »

Hi Di and Gengshi,

Thanks for bringing L-DNA to my attention. I've updated DSSR to v2.7.0-2025dec09, which automatically recognizes L-DNA/RNA steps. Using your model PDB (`b40-rb10.5_out_minimized_aligned2Z_i_x.pdb`) as an example, the new DSSR output is as follows:

Code: [Select]

  helix#1[1] bps=40
      strand-1 5'-AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG-3'
       bp-type    ||||||||||||||||||||||||||||||||||||||||
      strand-2 3'-TTTTTTTTTTAAAAAAAAAAGGGGGGGGGGCCCCCCCCCC-5'
      helix-form  LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
I’ve also tested it on PDB entry 4wb2, using biological unit 1 in the file 4wb2.pdb1, and the following output was obtained:

Code: [Select]

  helix#1[3] bps=9
      strand-1 5'-gcgugugug-3'
       bp-type    |||||||||
      strand-2 3'-cgcacgcac-5'
      helix-form  LLxL.xLx

Since L-DNA isn't a common form and DSSR may require further improvements to handle it better, I haven’t updated the documentation or the note in the DSSR output yet. Please let me know if the new DSSR output makes sense to you and share any questions or suggestions. Future updates to this feature would be much faster than this initial implementation.

Best regards,

Xiang-Jun

18

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: November 18, 2025, 09:25:57 pm »

Hi Di and Gengshi,

Thanks for the additional information. They are exactly the kind of information I was looking for.

• Glen Report 33-21: L-DNA: Applications and the Recognition of Mirror Image Nucleic Acids
• Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer (PDB entry 4WB3)

I'll study them carefully, and try to implement an option in DSSR to handle L-DNA atuomatically. I'll keep you updated.

Best regards,

Xiang-Jun

19

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: November 15, 2025, 10:31:55 am »

Hi Gengshi,

Thanks for your clarification regarding the naming of L-DNA, referring to the L-2-deoxyribose. It is a nice coincidence it is also left-handed.

Your L-DNA actually has prompted me to think more about this new (hypothetical) form of DNA, which is left-handed but with a B-type helix, by simply reversing x-coordinates of the classic B-DNA model. I can now have a clear mental image of this L-DNA: left-handed, with base-pairs flipped along the long axis. These are the two key features of Z-DNA, which characterizes a zig-zag backbone of CG repeats. The L-DNA, however, has a smooth backbone, as in B-DNA.

With this knowledge, it is not hard to classify L-DNA automatically with DSSR. I may consider to add the --L-DNA option specifically for this purpose, not to complicate the default DSSR output. It is after all not a common form, as A-, B-, and Z-form DNA. I would to see more examples of such L-DNA.

It is questions like yours that make DSSR more relevant and useful. I always appreciate users' feedback and encourage them to ask questions, sharing their experiences (both good and bad), freely and openly on the 3DNA Forum. Even in the age of AI, I still believe that there is no replacement for the human touch. I watch the 3DNA Forum closely and am quick to respond to users’ questions and concerns.

Best regards,

Xiang-Jun

20

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: November 11, 2025, 09:19:56 pm »

Hi Gengshi,

I've checked the two PDB files you uploaded: a standard B-DNA model (ending with aligned2Z.pdb), and its mirror-image (L-DNA), with x-coordinates negated (ending with aligned2Z_i_x.pdb). For clarity, I've extracted the first 6 atoms from each file, so readers easily see the differences.

# a standard B-DNA model          x
ATOM      1  P    DA A   1       0.621   9.421  -1.028  1.00  0.00           P
ATOM      2  O1P  DA A   1       0.606  10.783  -1.583  1.00  0.00           O
ATOM      3  O2P  DA A   1       1.439   9.186   0.166  1.00  0.00           O
ATOM      4  O5'  DA A   1      -0.863   8.945  -0.676  1.00  0.00           O
ATOM      5  C5'  DA A   1      -1.693   8.405  -1.689  1.00  0.00           C
ATOM      6  C4'  DA A   1      -2.528   7.255  -1.154  1.00  0.00           C

# a mirror-image, with x-coordinates negated
ATOM      1  P    DA A   1      -0.621   9.421  -1.028  1.00  0.00           P
ATOM      2  O1P  DA A   1      -0.606  10.783  -1.583  1.00  0.00           O
ATOM      3  O2P  DA A   1      -1.439   9.186   0.166  1.00  0.00           O
ATOM      4  O5'  DA A   1       0.863   8.945  -0.676  1.00  0.00           O
ATOM      5  C5'  DA A   1       1.693   8.405  -1.689  1.00  0.00           C
ATOM      6  C4'  DA A   1       2.528   7.255  -1.154  1.00  0.00           C

Mathematically, this is a simple operation, but you have created a hypothetical DNA type that is unknown to DSSR. Nevertheless, DSSR is functioning as intended:

• For the standard B-DNA model, DSSR classifies the dinucleotide step as 'B' correctly.
• For the L-DNA, DSSR cannot classify the dinucleotide steps. and designates them as '.' (see the section below). Also as noted in the header section, DSSR only recognizes the common A-, B-, and Z-form helices.

  Note: a helix is defined by base-stacking interactions, regardless of bp
        type and backbone connectivity, and may contain more than one stem.
      helix#number[stems-contained] bps=number-of-base-pairs in the helix
      bp-type: '|' for a canonical WC/wobble pair, '.' otherwise
      helix-form: classification of a dinucleotide step comprising the bp
        above the given designation and the bp that follows it. Types
        include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices,
        '.' for an unclassified step, and 'x' for a step without a
        continuous backbone.
      --------------------------------------------------------------------
  helix#1[1] bps=40
      strand-1 5'-AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG-3'
       bp-type    ||||||||||||||||||||||||||||||||||||||||
      strand-2 3'-TTTTTTTTTTAAAAAAAAAAGGGGGGGGGGCCCCCCCCCC-5'
      helix-form  .......................................

1. Is my understanding correct that DSSR can identify the geometry but does not recognize the form of our L-DNA?

Yes, that is correct. DSSR can see this is a left-handed helix, but it (currently) does not recognize your L-DNA form.

Along the line, one could imagine another form where y-coordinates are flipped. What would it be called? How would DSSR suppose to classify it?

2. Is there any way to make DSSR recognize the form of our L-DNA?

In principle, yes. One just needs to incorporate the domain-specific knowledge into the DSSR code. I need to know more about your L-DNA before considering how to do that.

Best regards,

Xiang-Jun

21

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: November 11, 2025, 12:41:46 am »

Hi Gengshi,

Thank you for sharing details about your L-DNA structure (mirror image of standard B-DNA). It seems to represent a novel form, and I plan to investigate it further. If feasible, I will update DSSR to accommodate this new form.

Best regards,

Xiang-Jun

22

MD simulations / Re: generate DNA pdb file for Gromacs

« on: September 13, 2025, 11:13:30 am »

Hi Mengyao,

Thanks for posting your question on the 3DNA Forum.

We are currently attempting to model non-natural nucleic acid structures. We would like to know if it is possible to predict the structure of threose nucleic acid (TNA). Is this feature already included in some of the tools ?

The main difference between TNA and DNA or RNA lies in the ribose. It is known that DNA (RNA) contains a pentose sugar, while TNA contains a tetrose sugar. Therefore, the connection sites of the phosphodiester bonds are different.

I am not familiar with TNA. From your description, TNA is a non-natural nucleic acid structure with a tetrose, instead of pentose, sugar. Given further information about TNA, I may be able to help build a model as a starting structure for MD simulations.

Best regards,

Xiang-Jun

23

MD simulations / Re: generate DNA pdb file for Gromacs

« on: September 13, 2025, 11:04:50 am »

The DNA pdb file generated by X3DNA has only A T C G, but no terminal base, e.g. A3, A5, T3, T5, ...
How to use X3DNA generate a pdb file with terminal bases?

DSSR has superseded X3DNA, and it can be used to generate a PDB file with terminal bases as you requested. See the following example:

Code: [Select]

# Generate a regular B-DNA model with sequence (AAAAAATTTTTT; shortened as A6T6)
x3dna-dssr fiber --b-dna --seq=A6T6 -o=A6T6-BDNA.pdb

# Mutate residue name 5'-A on chains A and B from the detault 'A' to 'A5':
x3dna-dssr mutate --entry='num=1 to=A5' -i=A6T6-BDNA.pdb -o=A5-both.pdb
A portion of the output PDB file A5-both.pdb is shown below:

REMARK PDB mutated using DSSR
REMARK DSSR mutate: A.A1 to A5
ATOM      1  P    A5 A   1      -0.356   9.218   1.848  1.00  0.00           P
ATOM      2  OP1  A5 A   1      -0.311  10.489   2.605  1.00  0.00           O
ATOM      3  OP2  A5 A   1      -1.334   9.156   0.740  1.00  0.00           O
ATOM      4  O5'  A5 A   1       1.105   8.869   1.295  1.00  0.00           O
ATOM      5  C5'  A5 A   1       2.021   8.156   2.146  1.00  0.00           C
ATOM      6  C4'  A5 A   1       2.726   7.072   1.355  1.00  0.00           C
ATOM      7  O4'  A5 A   1       1.986   5.817   1.352  1.00  0.00           O
ATOM      8  C3'  A5 A   1       2.952   7.370  -0.127  1.00  0.00           C
ATOM      9  O3'  A5 A   1       4.210   6.832  -0.518  1.00  0.00           O
ATOM     10  C2'  A5 A   1       1.848   6.598  -0.850  1.00  0.00           C
ATOM     11  C1'  A5 A   1       1.913   5.344   0.016  1.00  0.00           C
ATOM     12  N9   A5 A   1       0.717   4.478  -0.101  1.00  0.00           N
ATOM     13  C8   A5 A   1      -0.592   4.850  -0.293  1.00  0.00           C
ATOM     14  N7   A5 A   1      -1.424   3.839  -0.355  1.00  0.00           N
ATOM     15  C5   A5 A   1      -0.609   2.726  -0.193  1.00  0.00           C
ATOM     16  C6   A5 A   1      -0.886   1.349  -0.163  1.00  0.00           C
ATOM     17  N6   A5 A   1      -2.111   0.835  -0.301  1.00  0.00           N
ATOM     18  N1   A5 A   1       0.154   0.505   0.016  1.00  0.00           N
ATOM     19  C2   A5 A   1       1.380   1.020   0.154  1.00  0.00           C
ATOM     20  N3   A5 A   1       1.767   2.294   0.144  1.00  0.00           N
ATOM     21  C4   A5 A   1       0.712   3.105  -0.035  1.00  0.00           C
ATOM     22  P     A A   2       5.130   7.667  -1.527  1.00  0.00           P
ATOM     23  OP1   A A   2       5.914   8.669  -0.770  1.00  0.00           O
ATOM     24  OP2   A A   2       4.303   8.192  -2.635  1.00  0.00           O

In addition to the above question, is it possible to generate a pdb file that is fully compatible with Gromacs. Now there are some incompatible things. Such as Gromacs using DA, DT, DC, DG, rather than A, T, C, G.

I'm not sure the exact requirements for compatibility with Gromacs, but you can easily mutate 'A' to 'DA' etc using DSSR mutate subcommand as shown below:

Code: [Select]

x3dna-dssr mutate --entry='A:DA;T:DT' -i=A6T6-BDNA.pdb -o=DA-DT.pdb
See the DSSR User manual for more details.

24

MD simulations / Re: generate DNA pdb file for Gromacs

« on: September 13, 2025, 10:45:00 am »

Would you mind explaining to me how did you generate pdb file for your DNA sequence. I am new to this and stuck now on creating pdb file for my MD simulation. I will appreciate any kind of help here.

With DSSR (here v2.6.0-2025jul24 is used), you can use the following command to generate a PDB file for your (DNA) sequence:

Code: Bash

1. x3dna-dssr fiber --seq= A6C10 --repeat =2 --model =RNA
2. x3dna-dssr fiber --rna -o=rna -ss.pdb
3. x3dna-dssr fiber --rna -ds -o=rna - duplex .pdb # --rna -double , --RNA - duplex
4. x3dna-dssr fiber --g4 -o=g4.pdb
5.  
6. # The following four commands lead to the same results
7. x3dna-dssr fiber --seq= A6TC9 --repeat =2 -o=B1.pdb
8. x3dna-dssr fiber --B-DNA --seq= A6TC9 --repeat =2 -o=B2.pdb
9. x3dna-dssr fiber --model =b-dna --seq= A6TC9 --repeat =2 -o=B3.pdb
10. x3dna-dssr fiber --model =b-dna --seq=A6 -T-C9 --repeat =2 -o=B4.pdb
11.  
12. x3dna-dssr fiber --seq= A1000 --mmcif - output # B-DNA , in mmCIF output format
13.  
14. x3dna-dssr fiber --pauling --seq=A6 # three strands , all A6
15. x3dna-dssr fiber --pauling --seq=C6: # one strand : C6 ( A )
16. x3dna-dssr fiber --pauling --seq=A6:G2 # two strands : A6 ( A ) and G2 ( B )
17. x3dna-dssr fiber --pauling --seq=A6 :: G2 # two strands : A6 ( A ) and G2 ( C )
18. x3dna-dssr fiber --pauling --seq =: U3:G2 # two strands : U3 ( B ) and G2 ( C )
19. x3dna-dssr fiber --pauling -dna --seq=U8 --repeat =4 # U converted to T

See the DSSR User Manual, especially Section "5.2 Regular helical models (fiber)" for more details.

25

RNA structures (DSSR) / Re: Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« on: August 01, 2025, 09:03:27 pm »

Is there a way to directly generate a -fiber DNA helix with 10.5 bp/turn aligned to the Z-axis, avoiding parameter extraction and rebuilding?

The fiber model is based on experimental data, the details can be found via the following command: x3dna-dssr fiber --list

So the answer is NO with 3DNA/DSSR.

Best regards,

Xiang-Jun