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Xiang-Jun,
I just wanted to add that for simulations generated from CHARMM/NAMD that produce trajectory files in a binary format (sometimes named "DCD" files), one could use the MMTSB Tool Set:
http://blue11.bch.msu.edu/mmtsb/Main_Page (http://blue11.bch.msu.edu/mmtsb/Main_Page)
Click "Download" in the menu.
Although the MMTSB Tool Set was created in an effort to make simulating in CHARMM much easier, there is a script called "processDCD.pl" that, if used in the right way, can be used in conjunction with 3DNA (I've done this myself):
http://blue11.bch.msu.edu/mmtsb/processDCD.pl (http://blue11.bch.msu.edu/mmtsb/processDCD.pl)
I would be happy to share my experiences with using the MMTSB Tool Set.
Sean
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Hi Sean,
Thanks for sharing the info -- I came across MMTSB before, but did not get a chance to play with it. This is the first time I hear of the binary DCD trajectory files produced by CHARMM/NAMD. The Perl script "processDCD.pl" seems useful, too. I've downloaded MMTSB, and would like to spend some time to it.
I would be happy to share my experiences with using the MMTSB Tool Set.
That would be great! In addition to Alpay's Python script (which I have moved to this section), my Ruby scripts, now users will have access to a Perl version of analyzing MD trajectories using 3DNA! Please start a new thread in this "Molecular dynamics simulations" section; and remember to provide a concrete example so that others can follow. I'd also be interested in seeing an sample DCD file.
Best regards,
Xiang-Jun
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.