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Author Topic: Average or Global properties from a simulation  (Read 546 times)

Offline metoo

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Average or Global properties from a simulation
« on: March 23, 2017, 08:10:57 am »
Dear All

I am trying to extract some average properties from a 30-residue RNA duplex to distinguish between the A or the B form from a trajectory. I read the paper referenced by the admin earlier, but cannot find the documentation to extract the zp value or its distribution.

The second question pertains to extracting average (averaged over all base pairs) global properties over the entire double helix. Although this can be achieved with some additional scripts, I was hoping that there was already such an option present, so that one could extract, for example, the average radius of the helix (plusminus fluctuation), or the average zp parameter. Is there a user manual for 3DNA in place? I found the one for DSSR, but not 3DNA

Thank you in advance for the help, and I hope that I have not simply "not read the manual".

Best
Maria
« Last Edit: March 23, 2017, 08:25:56 am by metoo »

Offline xiangjun

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Re: Average or Global properties from a simulation
« Reply #1 on: March 23, 2017, 11:12:13 am »
Quote
I read the paper referenced by the admin earlier, but cannot find the documentation to extract the zp value or its distribution.

The output of Zp is in the main output file, in a section as below:

Quote
# find_pair 355d.pdb | analyze
# in the main output file: '355d.out'
# ---------------
Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases.

    step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 CG/CG   -2.24    8.78    0.37   -3.51    8.41    2.60     B
   2 GC/GC   -2.27    8.89    0.20   -0.59    8.76   -1.53     B
   3 CG/CG   -3.22    9.14   -0.51   -4.60    8.57    3.24     B
....

Quote
The second question pertains to extracting average (averaged over all base pairs) global properties over the entire double helix. Although this can be achieved with some additional scripts, I was hoping that there was already such an option present, so that one could extract, for example, the average radius of the helix (plusminus fluctuation), or the average zp parameter.

The 3DNA v2.3 distribution provides no option for averaging Zp parameters for a single structure, or an ensemble of NMR structures, or trajectories of MD simulations. For the analysis of MD simulations, the x3dna_ensemble script or do_x3dna may help.

Check a recent paper titled "Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations" which contains a section "PZ-containing DNA has properties associated with both B- and A-form DNA". Moreover, Robert Molt (the lead author) has kindly provided a post related to the work using 3DNA.

Quote
Is there a user manual for 3DNA in place? I found the one for DSSR, but not 3DNA

Check the $X3DNA/doc folder with the v2.3 distribution for available documentations. Short answer is: no up-to-date user manual for 3DNA (as the one for DSSR).

Hope this clarifies some of your confusions.

Xiang-Jun


PS. Curves+ from Dr. Richard Lavery is better integrated with analyses of MD simulations. You may want to give Curves+ a try, along with 3DNA.
« Last Edit: March 23, 2017, 12:40:21 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline metoo

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Re: Average or Global properties from a simulation
« Reply #2 on: March 24, 2017, 07:45:55 am »
Dear Xiang-Jun

Thank you very much for your replies. I ended up using some scripts to calculate a distribution of zp values over the simulation time. This will suffice for the time being !

Best

Maria

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.