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41

MD simulations / Re: generate DNA pdb file for Gromacs

« Last post by xiangjun 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DSSR has superseded X3DNA, and it can be used to generate a PDB file with terminal bases as you requested.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.

42

MD simulations / Re: generate DNA pdb file for Gromacs

« Last post by xiangjun 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.

43

MD simulations / Re: generate DNA pdb file for Gromacs

« Last post by ZMY on August 28, 2025, 07:05:11 am »

Dear all,

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.

Thank you in advance,
Best regards, Mengyao

44

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

« Last post by GengshiWu on August 03, 2025, 07:37:32 pm »

Hi Xiang-Jun,

Thank you for your response!

45

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

« Last post by xiangjun 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

46

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

« Last post by GengshiWu on August 01, 2025, 08:41:06 pm »

Hi Xiangjun,

Thank you for your explanation of the tilt in the rebuilt model,

To clarify our question, we extract parameters and rebuild because the B-DNA model generated with -fiber has 10 bp/turn, but we want a 10.5 bp/turn helix. To make it 10.5 bp/turn, we modify all twist values (except the last row) in dssr-B-DNA-A36-step.txt to 34.2857 (360°/10.5) before rebuilding.

Our goal is for the 10.5 bp/turn helix to align perfectly with the Z-axis, like the original fiber model. But as you noted, rebuilding positions the structure relative to its first base pair, causing some tilt.

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?

47

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

« Last post by xiangjun on August 01, 2025, 11:47:34 am »

Hi Gengshi,

Thanks for using DSSR and for posting your well-formulated question on the 3DNA Forum.

Could you please advise whether this tilt is expected due to reconstruction? Or is there a recommended way to maintain the original axis alignment during rebuilding?

Yes, the rebuilt structure and the original structure are in different coordinate systems, as expected. More specifically, the rebuilt structure is in the reference frame of the first base pair, while the original structure is in a whatever coordinate system it was originally in. For the fiber models from 3DNA/DSSR, base pairs grow from top to bottom, with decreasing z-coordinates. You can easily see this by looking at the dssr-B-DNA-A36.pdb file.

To put the two structures in the same coordinate system, you can use the --frame option of DSSR. Using your example, the command would be:

Code: Bash

1. # dssr-B-DNA-A36.pdb is the coordinate file from DSSR fiber model
2. x3dna-dssr -i=dssr-B-DNA-A36.pdb --frame=A.1:wc -o=expt-ref1.pdb

Now expt-ref1.pdb and the rebuilt structure dssr-B-DNA-A36-rb10.5.pdb would be in the same coordinate system. This is the simplest way to align the two structures. See the DSSR User Manual for more details.

It is also possible to transform the rebuild structure into the coordinate system of the original structure. It is a bit more complicated. I will consider write a blog post on this topic in the future.

You can easily verify that rebuild structure and the original structure are indeed very similar in two ways: One way is to re-analyze the rebuilt structure with DSSR, you will see that the base-pair parameters are very close to the ones for the original structure. The other way is perform a superimposition of the two structures, and  you will see that the RMSD for the base atoms is close to 0. See the commands below:

Code: [Select]

# extract base atoms from the original structure
x3dna-dssr -i=dssr-B-DNA-A36.pdb --select-base -o=exp-base.pdb

# extract base atoms from the rebuilt structure
x3dna-dssr -i=dssr-B-DNA-A36-rb10.5.pdb --select-base -o=rebuild-base.pdb

# the RMSD between exp-base.pdb and rebuild-base.pdb is 0.016.
For your verification, exp-base.pdb and rebuild-base.pdb are attached to this post.

While we're at it, here's an excerpt worth taking from the DSSR User Manual (5.3 Customized structures):

The 3DNA rebuild program complements analyze by reinforcing and verifying it. These two programs are a defining feature of 3DNA (Lu and Olson, 2003, 2008; Li et al., 2019). The 3DNA analyze and rebuild programs are based on SCHNAaP/SCHNArP (Lu et al., 1997a,b) which implement and extend the rigorous CEHS algorithm (El Hassan and Calladine, 1995) for the analysis/rebuilding of DNA duplexes.

The reversibility of the analysis/rebuilding programs in 3DNA allows scientists to ask what-if questions. By first deriving a complete set of base-pair parameters from an experimental structure, they can then systematically introduce changes in these parameters to see what happens to the shapes of the resulting 3D structures. This is a simple, yet powerful concept. 3DNA is the only widely used DNA/RNA structural bioinformatics tool with this feature. It has led to the discovery of a novel roll-and-slide mechanism to account for DNA folding in chromatin (Tolstorukov et al., 2007). Using modeling studies enabled by 3DNA, the Johnson lab at UCLA has revealed slide as a key parameter (along with roll and twist) in mediating DNA minor groove width (Hancock et al., 2019; Chen et al., 2018; Hancock et al., 2016, 2013; Stella et al., 2010).

The DSSR analyze module has completely surpassed the 3DNA analyze program (see Section 3.18). Similarly, the rebuild module in DSSR replaces the 3DNA rebuild program, with enriched functionality and improved usability. The module must be run as x3dna-dssr rebuild, just like a sub-command in Git.

48

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

« Last post by GengshiWu on July 31, 2025, 10:46:10 pm »

Hi Xiang-Jun, I have been working with the 3DNA DSSR tools to generate a B-DNA helix and encountered an unexpected issue with the axis alignment after reconstruction. Here are the steps that I performed:

1. Generated a 36 bp B-DNA helix using: x3dna-dssr fiber --model=B-DNA --seq=A36 -o=dssr-B-DNA-A36.pdb
    -When I open the dssr-B-DNA-A36.pdb file that I generated in UCSF Chimera, the helix axis aligns perfectly with the 3D coordinate z-axis.

2. Extracted parameters using: x3dna-dssr analyze --rebuild -i=dssr-B-DNA-A36.pdb -o=dssr-B-DNA-A36-expt.out
    -Then, I renamed the extracted step and helical parameter files for clarity: mv dssr-dsStepPars.txt dssr-B-DNA-A36-step.txt  mv dssr-dsHeliPars.txt dssr-B-DNA-A36-heli.txt

3. Reconstructed the structure using the step parameter file with: x3dna-dssr rebuild --backbone=B-DNA --par-file=dssr-B-DNA-A36-step.txt -o=dssr-B-DNA-A36-rb10.5.pdb
    - However, when I open the reconstructed pdb file in Chimera, the helix axis is slightly tilted relative to the z-axis.

Could you please advise whether this tilt is expected due to reconstruction? Or is there a recommended way to maintain the original axis alignment during rebuilding?

Thanks!

49

General discussions (Q&As) / Re: Download error for 3DNA v2.4.8-2023nov10 C Source Code

« Last post by nirtonik on July 27, 2025, 08:35:44 pm »

It is working, thank you so much!

50

General discussions (Q&As) / Re: Download error for 3DNA v2.4.8-2023nov10 C Source Code

« Last post by xiangjun on July 27, 2025, 04:48:46 pm »

Hi Arman Alborzi,

Thank you for reporting this issue, which has now been resolved. I am currently in the process of updating and reorganizing resources on our servers, which may cause temporary disruptions. Please try again and let me know if the problem persists.

Best regards,

Xiang-Jun