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Author Topic: analysis along the md trajectories  (Read 3545 times)

Offline aneeshcna

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analysis along the md trajectories
« on: July 21, 2010, 01:26:44 pm »
Dear 3DNA users,

I am using Amber 9.0 for MD simulation of B-DNA. I want to calculate the minor groove width along the 50ns length simulation.Is it possible to do such calculation with 3DNA  without generating snapshots (pdb files) at different time intervals?. Waiting for your valuable reply

Thanks in advance


Sincerely
Aneesh

Offline xiangjun

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Re: analysis along the md trajectories
« Reply #1 on: July 21, 2010, 10:16:16 pm »
3DNA per se does not (yet) have direct support for the analysis of MD simulation of nucleic acid structures; mostly because of my unfamiliarity with AMBER or other MD packages, up to this point. So you have to extract each snapshot in PDB format to analyze each separately, as you would normally do for a NDB/PDB entry. With some (Perl/Python/Ruby) script, this should be a straightforward/efficient process, I guess.

From literature, I know that 3DNA is increasingly being used (mostly) with AMBER to analyze MD trajectories. It would be very helpful to hear from those who have hand-on experiences; is there anyone willing to share? As noted in my blog post "3DNA in the PCCP nucleic acid simulations themed issue", I am more than willing to offer my help to make MD users' life easier.

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

Offline aneeshcna

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Re: analysis along the md trajectories
« Reply #2 on: July 22, 2010, 01:42:42 am »
Dear Dr. Xiang-Jun,

Thank you for the immediate reply.


Regards
Aneesh

Offline mfb

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Re: analysis along the md trajectories
« Reply #3 on: August 02, 2010, 02:45:45 pm »
Aneesh,

I am attaching two perl scripts that may be of use.  These will convert a group of pdb files created by ptraj and concatenate then into a single multi-model pdb file.  One version is for DNA where two strands are expected.  The other is for RNA, where a single chain is expected.  These scripts will convert the multi-letter base designations to one-letter designations and insert TER lines at the ends of chains. These are in-house and have only limited comments.

I had to change the extensions from the standard *.pl to *.txt in order to attach the files.

Mike Bruist (mfb)

Offline temizna

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Re: analysis along the md trajectories
« Reply #4 on: September 01, 2010, 05:47:28 pm »
I am attaching a python script that my be of use. I based this Python script on the code of  Yurong's X3DNA parser.


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

usage is: python parse3dna.py file NUMofSNAPSHOTS-1 NUMofBP
you will need to rename the *.out files to "file.NUM.out" where NUM is the snapshot number from nmr_strs output.
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.

Hope it helps.

Alpay

 

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.