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RNA structures (DSSR) / Analysis crashes: MD trajectory of abasic site in RNA
« on: August 22, 2018, 11:42:01 am »
Dear Xiang-Jun,
Thanks a lot for your work and support here.
I currently have two issues with DSSR:
1.
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:
2.
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
The frame seems to be ok in the pdb file (s. attachement). Do you have an idea of what might be going wrong?
Best,
Marcel
Thanks a lot for your work and support here.
I currently have two issues with DSSR:
1.
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:
Quote
x3dna-dssr -i=mod.pdb --nmr --json --abasic -o=mod.json
2.
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
Quote
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]
aborting...
The frame seems to be ok in the pdb file (s. attachement). Do you have an idea of what might be going wrong?
Best,
Marcel