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Author Topic: About output files from x3dna_md.rb  (Read 4112 times)

Offline Pablo Ricardo Arantes

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About output files from x3dna_md.rb
« on: September 07, 2012, 09:23:48 am »
Hello,

I runned the script x3dna_md.rb, and runned everthing fine! But I have some questions about the output files.
1º) The program generated a file, msgfile with these:

......Processing structure #1: <temp_model.inp>......
This structure has broken O3' to P[i+1] linkages
missing ' P  ' atom : residue name '  C', chain A, number [   1 ]
missing ' O1P' atom : residue name '  C', chain A, number [   1 ]
missing ' O2P' atom : residue name '  C', chain A, number [   1 ]
missing ' P  ' atom : residue name '  U', chain B, number [   1 ]
missing ' O1P' atom : residue name '  U', chain B, number [   1 ]
missing ' O2P' atom : residue name '  U', chain B, number [   1 ]
missing ' P  ' atom : residue name '  C', chain A, number [   1 ]
missing ' P  ' atom : residue name '  U', chain B, number [   1 ]

Time used: 00:00:00:00

Is this normal?

2º) The script generated only two files.out (temp_model.out, my RNA.out). In example folder in the x3dna_md folder, have 4 files .out (x3dna_md.out, x3dna_md2.out, x3dna_md3.out, x3dna_md4.out). I would like to know, If is everything normal with my analysis? The file .out generated, contains the results of all pdb from simulation as a example file.out.

I work in Gromacs program with Amber force field. I converted my trajectory, in separeted pdbs files such as example folder.

Thanks for your attention.

Pablo Ricardo Arantes

Offline xiangjun

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Re: About output files from x3dna_md.rb
« Reply #1 on: September 07, 2012, 12:31:11 pm »
Thanks for using 3DNA, and posting your questions on the forum.

Regarding your two questions:

1º) The missing atom messages are normal; they are for information only. "This structure has broken O3' to P[i+1] linkages" -- it means that there is an occurrence where nucleotides i and i+1 are not connected, as judged by out of range distance from O3'(i) to P(i+1). I am glad that you pay attention to this little detail. It may not be a concern -- you need to check a sample structure to be sure. If you need help, please attach such a structure with your follow up post.

2º) The two .out files are fine, and only 'RNA.out' is what you need. The example folder has four .out files correspond to the four different options:

Code: [Select]
  --ensemble, -e <s>:   Ensemble delineated with MODEL/ENDMDL pairs
    --models, -m <s>:   File containing an explicit list of model numbers
   --pattern, -p <s>:   Pattern of model files to process (e.g., *.pdb)
      --list, -l <s>:   File containing an explicit list of models

I am glad to see details on how 3DNA ('x3dna_md.rb' script) is being used.

Quote
I work in Gromacs program with Amber force field. I converted my trajectory, in separeted pdbs files such as example folder.

As noted above, the script can be run in four different modes, so you don't need to convert your trajectory into separate PDB files; the snapshots can be put into a single MODEL/ENDMDL delineated ensemble, as NMR structures in the PDB.

Note that in the current v2.1(beta), x3dna_md.rb has been replaced by x3dna_ensemble which has far more enhanced functionality. Please consider to update to the latest version.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Pablo Ricardo Arantes

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Re: About output files from x3dna_md.rb
« Reply #2 on: September 07, 2012, 10:07:09 pm »
Hi Xiang-Jun,

Thanks for all information! I'm glad that my analysis is fine.
Thanks for advices with the convertion of trajectory and the new version of x3dna_ensemble.

Best regards,

Pablo Ricardo Arantes

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.