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MD simulations / Re: About output files from x3dna_md.rb
« 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:
I am glad to see details on how 3DNA ('x3dna_md.rb' script) is being used.
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Note that in the current v2.1(beta), x3dna_md.rb has been replaced by x3dna_ensemble which has far more enhanced functionality.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
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