Messages

1

General discussions (Q&As) /

« on: April 12, 2007, 10:40:18 am »

My "misc_3dna.par" file does not have a 7th line.  It looks like this:
 
4.0  ON  A1  # upper H-bond length limit/atom, alternative location
8.5      # max. distance between paired base origins (FIND_PAIR)
2.5      # max. vertical distance between paired base origins (FIND_PAIR)
65.0    # max. angle between paired bases [0-90] (FIND_PAIR)
6.0      # MIN. distance between RN9/YN1 atoms (FIND_PAIR)
7.5      # max. distance criterion for helix break [0-12] (FIND_PAIR)

Do I need to add a new line, and if so, how should it read?

Thanks,
KDG

2

General discussions (Q&As) / DNA unwinding

« on: April 11, 2007, 03:47:01 pm »

I am trying to calculate the structural properties of a DNA sequence bound to an intercalating compound.  The DNA is a 15-mer with 7 correct base pairs on each side of a T-T mismatch in the middle of the sequence.  There is also a break in the DNA 5' to each of the Ts in the mismatched pair.  I would like to calculate the unwinding of the DNA using the global parameters based on C1'-C1' vectors.  I was able to obtain the global parameters for the unbound DNA, but 3DNA did not calculate them for the DNA with the compound bound (the output file only shows the deviation from regular linear helix).  Do you have any suggestions about how I might formulate my input file in order to obtain these parameters for the bound DNA?  Or do you have any suggestions for how I might be able to calculate the degree of unwinding using the other parameters?