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1

General discussions (Q&As) / find_pair problems with MD_Trajectory

« on: June 14, 2007, 04:36:30 pm »

I have been using X3DNA to analyze some MD simulations of a DNA/Protein complex. Initially I was running find_pair on each structure in a script but the program began dropping or not finding correct pairings.  Loosening the criteria for H-Bonds in the misc_3dna.par file seemed to help.  Base pairs at the ends of the DNA sequence cause most of the problems but we are not too concerned with these BP's.  We now have 20ns of simulated data and find_pair is missing BP's in the middle of the sequence which is what has prompted me to repost this problem.  My solution is to simply run find_pair once at the beggining of the simulation and use that generated pair listing which is correct for every structure.  I am testing this now but would like to know if there are any consequences of this hack?

Thanks, Levi Pierce

2

General discussions (Q&As) / find_pairs output

« on: October 10, 2006, 09:42:41 am »

Dr. Lu,

  Thanks for the quick response.  Is it possible to force find_pairs from reverseing the direction of base pairs.  For example:

 44  251  0 #   44 | -:..44_:[THY]T-----A[ADE]:.104_:-  0.98  0.91 27.73  8.86  1.31
   45  250  0 #   45 | -:..45_:[GUA]G-----C[CYT]:.103_:-  0.35  0.33 11.70  9.05 -0.49
   46  248  0 #   46 | -:..46_:[THY]T-*---T[THY]:.101_:-  1.48  1.02  9.88  9.32  3.51
   47  249  9 #   47 x -:..47_:[ADE]A-*---A[ADE]:.102_:-  6.37  4.93 16.04 10.30 16.23
   48  247  0 #   48 | -:..48_:[ADE]A-----T[THY]:.100_:-  0.91  0.88 36.14  9.06  1.17
   49  246  0 #   49 | -:..49_:[ADE]A-----T[THY]:..99_:-  0.91  0.88 51.76  8.99  1.18
   50  245  0 #   50 | -:..50_:[THY]T-----A[ADE]:..98_:-  1.10  1.01  8.23  9.02  1.63


I have been looking at the structure with VMD and it does look like a mess around these residue locations.  Just wondering if you have run into something similar.  I am using the following base-pair criteria
7.00 15.00  6.50 75.00  4.50  8.50

This is just one snapshot in the simulation and the other snapshots leading up to this and afterwards dont have this problem.  Out of about 250,000 snapshots approximately 6000 show a similar problem.  Thanks, Levi