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Topics - Marcel Heinz

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Dear Xiang-Jun,

Thanks a lot for your work and support here.
I currently have two issues with DSSR:

Do you have an idea why the backbone parameter for a nucleic acids are so much faster calculated with do_x3dna than with DSSR? Analyzing a trajectory with 100k frames take for a native structure approx. 2 hours with do_x3dna. A native RNA structure with DSSR will take approx. 10 days (10k frames/day). I need to run DSSR, because my system contains an abasic site.

I used this command line:

x3dna-dssr -i=mod.pdb --nmr --json --abasic -o=mod.json

I also run into problems with DSSR while trying to analyze a MD trajectory (100k structures) of a ~40 NA duplex structure, containing an abasic site. DSSR crashes with an error message at frame 1630 for the abasic site with the error message

model 1630 [1630 of 100000]
  1630.X.U.7          0.121
  1630.X.U.42         0.143
Uncaught exception 'Assertion failed' raised at [fncs_hbond.c:1762]

The frame seems to be ok in the pdb file (s. attachement). Do you have an idea of what might be going wrong?



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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.