Adenita exporting to oxDNA



  • Hi, I am new to SAMSON and Adenita. I would like to produce the initial configuration of a DNA motif for the oxDNA code. However, I have had some problems to export even simpler configurations (a dsDNA 5 bp long next to a ssDNA 10 nucleotides long). First, Adenita crashes if I try to export the workspace. Therefore, I export by selection; my selection is one of the followings (any node, any structural node, structural models) with the select-all mode. This selection makes that all particles change colour. After exporting, the two oxDNA files are created but they only show the information for the nucleotides in the dsDNA (10 atoms and 2 ss-strands). However, the topology file for oxDNA should contain 20 atoms and 3 strand types.

    The same happens if I have two ssDNA chains in the system (not hybridized or connected). The export creates the oxDNA files with the information for the first strand but not the second one.

    Are there any additional steps I need to consider before exporting the molecule? I would appreciate any help with this matter

    With kind regards,
    Yair

    Some additional information: I have tried this with SAMSON v 0.7.0 as recommended in github and also with SAMSON 0.8.5.



  • Dear Yair,

    Thank you for reporting the issues, I have identified the problem. The "Selected Part" option only handles one component for now, I will set this in upcoming updates to the entire selection. One possible workaround is to merge both strands into a single component after creating them with the "Merge Editor". If you encounter any other crashes let me know, in case you have a github account you can open a ticket (I think) a there too.

    Best regards,

    Elisa



  • Dear @Yair-Augusto, Adenita was just updated and this problem should have been fixed. Please let me know if it persists or you find new ones.

    Best regards,

    Elisa


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