Recent Posts

31

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by xiangjun on March 13, 2025, 03:56:04 pm »

Thanks for your quick follow-up.

As noted in the x3dna_utils cp_std -h help message, the utility covers the most common use cases:

Select the standard data files to be used with "analyze" and "rebuild".
Available sets include BDNA, ADNA, NDB96 and RNA, which have exactly
the same base geometry and orientation (in the standard base reference
frame) but different backbone conformations.

Z-DNA is different from the standard right-handed DNA/RNA double helix in that it has not only a left-handed twist but also a base flip, and it has a di-nucleotide (most commonly CpG) as a the building block. So the x3dna_utils cp_std does not cover Z-DNA. However, you can run analyze, modify the output parameters (and extend as needed), and then rebuild a Z-DNA structure according to the modified parameters.

What specific Z-DNA structure you’d like to extend? If you do not want share details, please use a sample Z-DNA structure that helps illustrate your point. Reproducibility is important.

Best regards,

Xiang-Jun

32

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by shr on March 13, 2025, 02:23:03 pm »

I have a PDB structure of Z-DNA-protein complex that I wanted to simulate. Before simulation, I wanted to make the DNA longer to avoid the issue of the protein interacting with any of the terminal bases. I can use the following commands to achieve this in case of B-DNA:

find_pair 1MNN.pdb 1mnn.bps
x3dna_utils cp_std bdna
rebuild -atomic bp_step.par extended_dna.pdb

But x3dna_utils does not take zdna as an argument so I was wondering how I can do it?

33

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by xiangjun on March 13, 2025, 02:14:06 pm »

Hi,

Thanks for using 3DNA and for posting your questions on the Forum. 3DNA rebuild should be able to build Z-DNA structures given a set of parameters. Please be specific with what you are trying to achieve, and we can start from there.

Best regards,

Xiang-Jun

34

General discussions (Q&As) / Rebuilding Z-DNA

« Last post by shr on March 13, 2025, 02:10:17 pm »

I was wondering if there is a way to rebuild Z-DNA with rebuild module in the local installation of x3DNA. I know it works for B-DNA and A-DNA and I can make a Z-DNA fiber model as well but I couldn't find a direct way to extend an existing Z-DNA structure. Is there a workaround which I can try? Thank you in advance.

35

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« Last post by xiangjun on February 28, 2025, 08:47:06 am »

Welcome back.

But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

Are you expecting 3DNA/DSSR to "generate the PDB" by specifying the residues, including unknown ones?  3DNA/DSSR can build DNA/RNA structures with standard bases (A,C,G,T,U), or modified ones with *known* building block as illustrated in 5-methylcytosine in the FAQ. It does not generate structures for ligands like m3C. It is up to the user to provide such building blocks for 3DNA/DSSR to proceed. CCP4 and Phenix may have utilities to generate new ligands.

By the way, what does PSF stand for?

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

Sorry, I'm not familiar with this field, and I cannot offer any valuable suggestions. Overall, this question is out of the scope of the Forum.

Best regards,

Xiang-Jun

36

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« Last post by Sunera on February 27, 2025, 11:24:32 pm »

Hi Dr. Jun,

Sorry for the late reply. Yes, I definitely think the idea in the FAQ is relevant. But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

37

MD simulations / Re: Update of do_x3dna package

« Last post by xiangjun on February 22, 2025, 11:23:27 pm »

Hi Rajendra,

Thanks for the update to do_x3dna for GROMACS-2025. It is great that the "binary package can be used with files generated by any version of GROMACS". Over the years, I've received emails about applying 3DNA to MD simulations, and I know that your do_x3dna package is well received by the community.

Best regards,

Xiang-Jun

38

MD simulations / Update of do_x3dna package

« Last post by rkumar on February 22, 2025, 11:12:53 pm »

Dear All,

I have updated the do_x3dna package for GROMACS-2025. I have built binary executable of do_x3dna that can be downloaded and used without any compilation. Most importantly, this binary package can be used with files generated by any version of GROMACS.

Thanks,
Dr. Rajendra Kumar
Associate Professor
NIPER, Mohali, India

39

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« Last post by xiangjun on February 07, 2025, 10:22:26 am »

Hi Jing,

Please follow what I suggested in the previous response. As for the 3DNA source code, did you notice the download link at the top and the Download instructions post?

Best regards,

Xiang-Jun

40

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« Last post by azurelegend on February 06, 2025, 09:23:25 pm »

Hi Xiang-Jun,

Thank you so much! I'll take time to explore on it. By the way, last time you said the 3DNA source code is available, where could I find it?

Best,
Jing