Messages

1

MD simulations / Re: Problem with x3dna_ensemble analyze

« on: November 23, 2016, 12:13:11 pm »

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

2

MD simulations / Re: Problem with x3dna_ensemble analyze

« on: November 22, 2016, 12:48:02 pm »

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

3

MD simulations / Re: Problem with x3dna_ensemble analyze

« on: November 22, 2016, 12:14:30 pm »

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

4

MD simulations / Problem with x3dna_ensemble analyze

« on: November 22, 2016, 11:51:19 am »

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