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MD simulations / local helical axis vector for strongly bent DNA
« on: June 20, 2017, 06:49:53 pm »
Hello everyone,
I was analyzing a molecular dynamics simulation (http://www.amber.utah.edu/FF-DNA-bsc1-OL15/3GGI/opc/bsc0/ ) with do_x3dna and noticed, that in the HelAxis_g.dat file for most of the frames one line of data is missing. (sometimes even two lines are missing or replaced by '----'). The DNA contains 10 base-pairs, so there should be 9 helical axis vectors, since they are calculated as base-step parameters.
When I run single frames of the simulation with X3DNA, and look at the local helical axis vector there, I find four different cases.
1. "number of base-pairs: 10" ; all helical axis vectors are calculated.
2. "number of base-pairs: 9" ; the helical axis vector for one base-pair step is missing.
3. "number of base-pairs: 8" ; the helical axis vectors for two base-pair steps are missing.
4. "This structure has broken O3'(i) to P(i+1) linkages" and "number of base-pairs: 9" ;
the helical axis vector of one base-pair step is missing and in another line the data is replaced by '----'.
My explanation for this is, that if the program detects a broken base-pair, it refuses to calculate any vectors and prints '----' instead. Also it seems, that if the DNA is deformed or broken too much, then the program doesn't recognize this as a base-pair anymore and thinks the DNA is shorter than it actually is.
My question is now: Is there any way to force the program to still calculate a helical axis vector, even if the DNA is strongly bent and/ or broken?
And if yes, does maybe someone know, how to implement this into the do_x3dna program?
Thank you very much for your help,
Adina
I was analyzing a molecular dynamics simulation (http://www.amber.utah.edu/FF-DNA-bsc1-OL15/3GGI/opc/bsc0/ ) with do_x3dna and noticed, that in the HelAxis_g.dat file for most of the frames one line of data is missing. (sometimes even two lines are missing or replaced by '----'). The DNA contains 10 base-pairs, so there should be 9 helical axis vectors, since they are calculated as base-step parameters.
When I run single frames of the simulation with X3DNA, and look at the local helical axis vector there, I find four different cases.
1. "number of base-pairs: 10" ; all helical axis vectors are calculated.
2. "number of base-pairs: 9" ; the helical axis vector for one base-pair step is missing.
3. "number of base-pairs: 8" ; the helical axis vectors for two base-pair steps are missing.
4. "This structure has broken O3'(i) to P(i+1) linkages" and "number of base-pairs: 9" ;
the helical axis vector of one base-pair step is missing and in another line the data is replaced by '----'.
My explanation for this is, that if the program detects a broken base-pair, it refuses to calculate any vectors and prints '----' instead. Also it seems, that if the DNA is deformed or broken too much, then the program doesn't recognize this as a base-pair anymore and thinks the DNA is shorter than it actually is.
My question is now: Is there any way to force the program to still calculate a helical axis vector, even if the DNA is strongly bent and/ or broken?
And if yes, does maybe someone know, how to implement this into the do_x3dna program?
Thank you very much for your help,
Adina