average values from MD simulations

[ara]

Hello,

I have been using 3DNA for about a month now and find it very useful especially after the Ruby scripts for MD analysis came out. Thank you!

I am using the program to analyze drug-DNA MD simulations and would like to plot base pairs vs Twist (or Rise or Roll) values and therefore I would like to find an average of those values for each base pair over the simulation. Does bp_helical or bp_step provide that kind of info? Or I will need to write my own script for that?

Please let me know if my question is unclear - I will try to clarify it better.

Thanks in advance!

Ara

[xiangjun]

Hi Ara,

Thanks for using 3DNA, and for posting your question(s) in the forum. I am glad to hear that you found the Ruby scripts useful to your analysis of drug-DNA MD simulations -- at the very least, I take it as yet another user confirmation that the Ruby scripts are working as expected.

I am using the program to analyze drug-DNA MD simulations and would like to plot base pairs vs Twist (or Rise or Roll) values and therefore I would like to find an average of those values for each base pair over the simulation. Does bp_helical or bp_step provide that kind of info? Or I will need to write my own script for that?

Again, since I have no direct MD-simulation experience, my understanding could be incomplete. If I guess it correctly, your MD simulations should include many snapshots. The output file for each parameter (e.g.,[mono:1b7xkmyt]x3dna_md_roll.out[/mono:1b7xkmyt] for Roll) from the Ruby scripts, [mono:1b7xkmyt]x3dna_md.rb/extract_par.rb[/mono:1b7xkmyt], contains tabulated values arranged in a m-by-n matrix, where m is the number of models/snapshots, and n is the number of base-pair steps. As noted in the initial release post, "The output parameter table is intended to be fed into R/Matlab/Octive/Excel etc for statistical analysis or visualization." Specially, I decided deliberately not to calculate mean/std etc statistics, even though it should be straightforward to add them.

On the other hand, the files "bp_helical.par" and "bp_step.par" are from each run of the [mono:1b7xkmyt][red:1b7xkmyt]analyze[/red:1b7xkmyt][/mono:1b7xkmyt] program on a snapshot, i.e., they are from native 3DNA output, and are overwritten each time unless you renamed them. Put another way, these two files are not related to your MD analysis; instead they are intended to be used with the [mono:1b7xkmyt][red:1b7xkmyt]rebuild[/red:1b7xkmyt][/mono:1b7xkmyt] program to construct DNA structures as specified by the parameters.

HTH,

Xiang-Jun

[temizna]

Hi Ara

As Xiang-Jun suggested, you can use R and load your twist/roll data as matices to R. then by simply using colMeans function you can get the simulation means for each step as a vector and plot it.

HTH,
Alpay

[ara]

Thank you very much Xiang-Jun and Alpay for your responses.

I have two more questions though:

In my simulation I have a quite large opening of an AT base pair and a consecutive breaking of one of the hydrogen bonds between this pair. And I want to check if it is only T that is opening and stretching away from A or not. So I was wondering if 3DNA can give information on which base exactly is fluctuating more causing the opening in the pair or it can give information only on a base pair in this case?

My other question is about bending angle calculation. I know you have come across this question several times in this forum but my main issue is if I can calculate the DNA bending during the simulation time or I will need to find an average structure of my simulation and calculate the bending of that structure.

Thanks a lot in advance!

Ara

[xiangjun]

Hi Ara,

Welcome back.

So I was wondering if 3DNA can give information on which base exactly is fluctuating more causing the opening in the pair ?

No. 3DNA "can give information only on a base pair in this case".

if I can calculate the DNA bending during the simulation time

No.

or I will need to find an average structure of my simulation and calculate the bending of that structure.

It is entirely up to you. Please remember that 3DNA is just a tool set.

See my blog post "Calculation of DNA bending angle " for more information.

HTH,

Xiang-Jun