oxDNA export

[zoombya]

The exported structure has no base-pairing in oxDNA and many overlaps. Taco oxDNA converted file for reference:

[thenlevy]

Thank you for reporting this.

Is this a designed imported from cadnano to ENSnano, and then converted from ENSnano to oxDNA ? In that case the problem might be that ENSnano does not position correctly the helices during the import from cadnano. In that case the overlapping should also be visible in the 3D view of ENSnano.

Could you provide the cadnano file ?

[zoombya]

Here is a simplified test tile, from cadnano SQ. Yes I'm using the ENSnano import and than do an export. I'm using the windows version. test_tile.zip

[thenlevy]

I loaded your example and I think the problem could actually be due to the fact that I missunderstood the oxDNA format.

In the oxDNA configuration file, a position for each nucleotide must be given. I thought that this position were the "backbone position" (position of the sugar) , while it might actually be the position of the base.

ENSnano is therefore producing oxDNA files in which the radius of the helices is too large. This should not be too difficult to fix.

I see that you are an oxDNA contributor. Do you know if the base-to-backbone distance is constant in oxDNA and what is the value of that constant ?

[thenlevy]

It actually seems that the position that must be written in the cofinguration file is neither that of the backbone nor that of the base, but the position of the center of mass. I found the formula to convert backbone position to center of mass position in taco oxDNA.

Could you check on the branch fix_oxdna_export if the export now look correct to you ? Here is a compiled executable for windows of that branch ensnano_fix_oxdna_export.zip

[zoombya]

Hi, thanks for the quick reply and effort. You are much closer now, but you most likely have a problem with the a-vectors. Possibly ox-views / Dynamics / Forces / Create from Base pairs feature might be of help to you. It creates Force traps between bases which are connected, but fails on the test structure.

Also this colab lets you run an online instance of oxDNA so you can check if the design explodes. (with this design forces are needed). https://colab.research.google.com/drive/1nFC9zy-wEwwl8vlJZAbQZZofavP4PXvL#scrollTo=C_8TB2t5gxDg

[thenlevy]

I think I have fixed the problem with the a-vectors. The problem was that for the vector a1 I used the backbone to helix axis vector, while I needed the backbone to base vector. I have been able to use the colab to run a simulation of the design exported with ENSnano

Here is a compiled executable for windows of that branch ensnano_fix_oxdna_export.zip

[zoombya]

great thanks ;)

[thenlevy]

fixed by #6