Re: [AMBER] cpptraj + nastruct

From: Thomas C. Bishop <>
Date: Thu, 26 May 2016 07:49:38 -0500

   Good to hear from you Vlad.
   I had been using X3DNA but last I checked 3DNA could not read DCD's only
   pdbs so processing is slow.
   ( I have some vmd scripts that automate 3DNA analysis if anyone's
   interested... but it's not terribly efficient)
   We tested cpptraj yesterday and I was _amazed_ at how fast it is compared to
   cpptraj has advantage over Curves/3DNA that it can do a lot of analysis in
   one run.
   I still need to compare to what Curves offers.

   On 05/26/2016 02:33 AM, Vlad Cojocaru wrote:

     Dear Tom,
     We are using Curves or X3DNA to do this type of analysis. These programs
     recognize automatically the base pairs and give you all data you need
     regarding the DNA helix. As I don't have experience with nastruct in
     Cpptraj, I cannot say if the functionality is as good as in these 2
     programs but as these 2 were made especially for this type of analysis,
     I'd expect the functionality is superior to Cpptraj which is a more
     general analysis tool. But sure, I may be wrong ...
     Best wishes
     On 05/26/2016 01:31 AM, Thomas C. Bishop wrote:

         Dear Amber,
         I'm using CPPTRAJ to analyze some simulations w/ dsDNA and want to
         helical parameter data w/ nastruct.
         Is there any other method than using a reference structure for having
         nastruct identify the base pairs.
         Specifically can I tell nastruct which residues are paired with which?
         Pointers to tools for statistically summaries of the results would be
         Thanks in advance,

   Thomas C. Bishop
    Tel: 318-257-5209
    Fax: 318-257-3823
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Received on Thu May 26 2016 - 06:00:02 PDT
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