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Author Topic: A modified 3DNA parser for MD trajectory analysis  (Read 3636 times)

Offline temizna

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A modified 3DNA parser for MD trajectory analysis
« on: January 07, 2011, 06:50:10 pm »
I am attaching a python script that my be of use for trajectory analysis. I based this Python script on the code of Yurong's X3DNA parser.

Recipe:
First run nmr_strs program on your trajectory (save trajectory as one pdb file)
The python program parses the .out files generated by nmr_strs
>  nmr_strs --pdbfile test.pdb
> csh mv.txt
     script to rename files:
     you will need to rename the *.out files to "file.NUM.out" where NUM is the snapshot number from nmr_strs output.
        Example:
     mv testNUM.out test.NUM.out
     where NUM is the snapshot number.

> python parse_3dna_out.py file NUMofSNAPSHOTS NUMofBP
> python parse_3dna_out.py test 20 12
usage is: python parse3dna.py file NUMofSNAPSHOTS NUMofBP
The test file contains 100 ps snapshots from a 2 nanosecond simulation trajectory of a DNA hairpin. (20 snapshots)
NUMofSNAPSHOTS is the total number of snapshots read in nmr_strs program
NUMofBP is the number of base pairs identified for the trajectory.

This will create csv files along the trajectory for each base pair (as columns excluding the end base pair where the values are 0 or not calculated)

You can open csv files with excel or any other program.

Hope this helps,
Alpay

Offline xiangjun

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Re: A modified 3DNA parser for MD trajectory analysis
« Reply #1 on: January 07, 2011, 09:30:39 pm »
Hi Alpay,

Thanks for your contribution! Hopefully, more 3DNA users would share their experiences through the forum.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.