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MD simulations / Stacking of two neighboring non-base-paired bases
« on: January 26, 2013, 05:54:53 pm »
Dear Dr. Lu and X3DNA users,
I am relatively new to X3DNA, and am trying to use the x3dna_md.rb and extract_par.rb to analyze stacking and sliding of two neighboring bases in my RNA MD simulations. I've successfully used x3dna_md.rb on PDB files of each frame of one of my MD simulations, but I'm thinking this might not be the best way to analyze my data. I believe that since the two bases I'm interesting in monitoring are not in base pairs themselves, they would be missed by find_pair. I was thinking that the analyze script might be a way to go, but if I'm not mistaken, analyze also takes the output of find_pair for its input.
Any help that can be provided would be much appreciated! Please also do let me know if there are threads that have already addressed my concern; I have looked for these but may have missed them.
I am relatively new to X3DNA, and am trying to use the x3dna_md.rb and extract_par.rb to analyze stacking and sliding of two neighboring bases in my RNA MD simulations. I've successfully used x3dna_md.rb on PDB files of each frame of one of my MD simulations, but I'm thinking this might not be the best way to analyze my data. I believe that since the two bases I'm interesting in monitoring are not in base pairs themselves, they would be missed by find_pair. I was thinking that the analyze script might be a way to go, but if I'm not mistaken, analyze also takes the output of find_pair for its input.
Any help that can be provided would be much appreciated! Please also do let me know if there are threads that have already addressed my concern; I have looked for these but may have missed them.