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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
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