Messages

1

MD simulations / dna torsional angle wheels

« on: December 13, 2013, 11:40:10 am »

Hi everyone,

I was wondering if anyone is aware what would be best program to plot these kind of torsional angle wheels -- http://maptest.rutgers.edu/drupal/files/oldimages/images/stories/author/nthtung/B_DNAimg/wheel.jpg

i like it as one can see all torsional angle distributions in one plot. I would like to do this for my molecular dynamics data. I have tried with gnuplot or origin but could not find a way to do that. Also I know about the "Dials and Windows" program but not sure if it can do that or where to download it.

Any help is appreciated,

Thanks,

Ara

2

General discussions (Q&As) / Re: old Curves?

« on: July 27, 2013, 04:14:03 pm »

Thank you Xiang-Jun!

I did contact Dr. Lavery, however have not heard back from him yet. And thank you for the information about Dr. Rohs!

Ara

3

General discussions (Q&As) / old Curves?

« on: July 26, 2013, 05:17:07 pm »

Dear 3DNA community,

I know this is a 3DNA forum, however, I have a question about Curves. I did not find any Curves forum and I really like this forum and found it helpful in many ways.
I am analyzing DNA bending from molecular dynamics trajectories based on crystal structure of a drug-DNA complex. The crystal structure DNA bending was calculated with the old Curves program (Curves 5.2). I wanted to also use this old Curves for calculating DNA bending but I could not find it online. I do see some research groups that use both Curves and Curves+ to compare their results (A measure of bending in nucleic acids structures applied to A-tract DNA. F. Lankaš, N. Špačková, [...], and J. Šponer. Nucleic Acids Res. 2010 June; 38(10): 3414–3422). So i was wondering if anyone is aware if the old Curves is still available? Or currently there is only Curves+?

Thank you in advance,

Ara

4

MD simulations / Re: average values from MD simulations

« on: March 19, 2011, 11:39:58 pm »

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

5

MD simulations / average values from MD simulations

« on: February 27, 2011, 08:52:47 pm »

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