3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: slaw on December 08, 2010, 05:09:51 pm

Title: Missing Groove Measurement
Post by: slaw on December 08, 2010, 05:09:51 pm: Hi All,

I am calculating the major and minor groove distances using 3DNA from different snapshots from an MD simulation. I noticed that in one snapshot 3DNA reports the major/minor groove measurements for 16 base pairs and in a later snapshot 3DNA only reports major/minor groove values for 15 base pairs. I should point out that there are significant dynamics in my DNA molecule that is correlated with the missing base pair but, according to the documentation, major/minor groove distances are measured based upon the P-P distance and does not depend on the helical axis. Is there a way to force the program to calculate all such values regardless of the dynamics of the DNA? Or is it possible to tell 3DNA exactly which bases are paired and to use the same information for all snapshots from the simulation.

Thanks,

Sean
Title: Re: Missing Groove Measurement
Post by: slaw on December 08, 2010, 05:18:22 pm: Hi,

I found this blog post by Xiang-Jun that discusses exactly this topic:

http://xiang-jun.blogspot.com/2010_07_18_archive.html (http://xiang-jun.blogspot.com/2010_07_18_archive.html)

I will report back with my experience.
Title: Re: Missing Groove Measurement
Post by: xiangjun on December 08, 2010, 09:07:26 pm: Hi, Sean:

Hopefully the blog post you referred to, "3DNA for the analysis of molecular dynamics simulations (http://http://xiang-jun.blogspot.com/2010/07/3dna-for-analysis-of-molecular-dynamics.html)", helps solve your problem. If any thing is still unclear, please provide a concrete example case.

Xiang-Jun
Title: Re: Missing Groove Measurement
Post by: slaw on December 09, 2010, 12:59:05 pm: Hi all,

Yes, the blog explained exactly what I needed to do.

1) Generate an input file using find_pair
2) Use this input file in the analyze program for all frames

Thanks again!
Title: Re: Missing Groove Measurement
Post by: temizna on December 13, 2010, 01:49:26 pm: Then you need to parse the out files to get the time series info for each parameter you want to further analyze. 3DNA does not output time series data. May be in the future! :)