find_pair problems with MD_Trajectory

[elpierco]

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

[xiangjun]

As explained in my reply to your original question, what you now propose to do is perfectly fine. It is actually the preferred way for MD trajectories and NMR ensembles, where the DNA structure changes only in conformation not in its base-pairing. You can thus start with a representative structure to derive the correct pairing information with "find_pair" (and make manual changes where necessary), and you then need only to change the first two lines (PDB file and corresponding output file) of the input file to "analyze/cehs". Of course, this is best done automatically with a script.

The program "find_pair" makes analyzing nucleic acid structure so easy that people normally use it together with "analyze/cehs" as an integrated unit. As a matter of fact, "find_pair" has more functionalities (as another application, see SWS from Pascal Auffinger) than just providing input to the analysis routines, and it is best to think them as two separate entities.

Based on my experience, "find_pair" has been working really great for what it was designed for. Over the years, it has been refined and thus become more robust and sophisticated in the coming new release of 3DNA v2.0. At this time, I feel confident to say that whenever "find_pair" (and accordingly "analyze/cehs") produces some weird base-pairing results, it is because the nucleic acid structure is too distorted in the corresponding region(s). Whenever in doubt, it certainly helps to have a look of your structure using a molecular viewing program such as Rasmol/Pymol.

As always, we welcome users' feedback for specific cases where the algorithm could possibly be improved. That's why I asked you to send me some structures you felt that "find_pair" was not working as expected. To make life easier for future communications, I have installed the phpBB2 "Attachment Mod" for this forum. Please make good use of it!

HTH,

Xiang-Jun