Problem with x3dna_ensemble analyze

[aimeeli66]

Dear 3DNA users,

When I tried to use x3dna_ensemble analyze to deal with my trajectory ( a pdb file including many frames/models generated by gromacs), I met this error:

x3dna_ensemble analyze -s -e md_100.pdb
Process model #1   1 / 101
Process model #2   2 / 101
Process model #3   3 / 101
Process model #4   4 / 101
Process model #5   5 / 101
Process model #6   6 / 101
Process model #7   7 / 101
Process model #8   8 / 101
Process model #9   9 / 101
Process model #10   10 / 101
Process model #11   11 / 101
Process model #12   12 / 101
Process model #13   13 / 101
Process model #14   14 / 101
Process model #15   15 / 101
Process model #16   16 / 101
Process model #17   17 / 101
Process model #18   18 / 101
Process model #19   19 / 101
Process model #20   20 / 101
Error in running command: '/home/shuting/Downloads/x3dna-v2.3/bin/analyze  temp_model.nts 2> msgfile'
Rerun the command w/o redirection for details

I also tried  x3dna_ensemble analyze -b rna.dat -e md_100.pdb, and met the same problem.
I am not sure about why it happened. I was wondering whether there is some default setting for 20 models (like the example) only. I am using Ubuntu. Or is it because how I installed the software?

I tried   x3dna_ensemble analyze -t -e md_100.pdb. It seems to process all the models but there is still a problem.
 x3dna_ensemble analyze -t -e md_100.pdb
Process model #1   1 / 101
Process model #2   2 / 101
Process model #3   3 / 101
Process model #4   4 / 101
Process model #5   5 / 101
```````
Process model #100   100 / 101
Process model #101   101 / 101
/home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:74:in `block (4 levels) in write_out_parameters': undefined method `sub' for nil:NilClass (NoMethodError)
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:74:in `map'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:74:in `block (3 levels) in write_out_parameters'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:71:in `each'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:71:in `each_with_index'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:71:in `block (2 levels) in write_out_parameters'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:69:in `each'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:69:in `block in write_out_parameters'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:63:in `open'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:63:in `write_out_parameters'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:124:in `process_ensemble_models'
   from /home/shuting/Downloads/x3dna-v2.3/lib/ensemble.rb:54:in `main'
   from /home/shuting/Downloads/x3dna-v2.3/bin/x3dna_ensemble:37:in `<main>'

Has anyone ever dealt with this kind of problem? I am new to 3DNA and it's the first time to use ruby script. Help will be very appreciated!

Sincerely,
Shuting

[xiangjun]

Could you please provide a (minimal) reproducible example?

Thanks,

Xiang-Jun

[aimeeli66]

Dear Dr. Lu,

I couldn't upload my trajectory here because the file is larger than the maximum allowed for attachment. The attachment is the first model. Is there another way I can show you my file? Thank you!

Sincerely,
Shuting

[xiangjun]

Hi Shuting,

You do not need to upload the whole trajectories of your molecular dynamics (MD) simulations, just enough frames (is this the right word?) to illustrate the problem. From your first post, I noticed that the script broke after the 20th model. So maybe you can extract models 18 to 22 that will still reproduce the issue. Asking a reproducible question is the first step others can help you answer it.

Hope this makes sense.

Xiang-Jun
 

[aimeeli66]

Dear Dr. Lu,

Thank you so much! I attached the pdb file with model 18 -22. And I tried the same command. The same problem did appear.

x3dna_ensemble analyze -s -e md_18_22.pdb
Process model #18   1 / 5
Process model #19   2 / 5
Process model #20   3 / 5
Error in running command: '/home/shuting/Downloads/x3dna-v2.3/bin/analyze  temp_model.nts 2> msgfile'
Rerun the command w/o redirection for details

Sincerely,
Shuting

[xiangjun]

Thanks for your follow-up. I will look into the issue and report back on the Forum, hopefully in the near future.

Best regards,

Xiang-Jun

[xiangjun]

Hi Suting,

I've checked the models (no.18-22) you uploaded. An image of model no. 20 is attached, which shows clearly that G4, G5, and C26 are split apart. Especially, G4 can no longer be taken as a purine due to incomplete base ring atoms, which explains why the x3dna_ensemble script stops at this entry. Similar issues happen with models #19 and #22, whilst models #18 and #21 look fine. Please double check your procedure on how the MODEL/ENDMDL-delinated ensemble of MD models are generated.

In this case, as in several scenarios I am aware of, 3DNA is helpful in identifying inconsistencies in the analyzed dataset. Care must be taken to ensure sensible results in an otherwise complicated process/pipeline.

HTH,

Xiang-Jun

[aimeeli66]

Dear Dr. Lu,

Thank you so much! Yes, you are so right, the problem is caused by my models because the molecule ran out of the box during the simulation. I need to do something and put it back in center.

Sincerely,
Shuting