Re: [AMBER] cpptraj + nastruct

From: Thomas C. Bishop <>
Date: Thu, 26 May 2016 14:27:42 -0500

   Amber, Vlad, Dan,
   Thanks for replies. I 'm trying to determine optimal path forward.
   Comparison: Curves, 3DNA, nastruc
   1) Structure info: All provide same analysis (except Nastruct missing global
   axis and goovecalc(?))
   2) All can do "automatic" base pair recognition (curves too?)
   3) 3DNA and Curves allow manually assigning the base pairs
   4) ONLY nastruct (via cpptraj can read traj, crd, pdb , AND dcd)
   5) statistics:
   Curves comes /w Canal for statistical analysis and propery handles circular
   nastruct can use cpptraj data analysis commands
   3DNA (roll your own stats?)
   6) rebuilding ?
   I'm less certain about rebuilding atomic or coarse grained models
   3DNA yes no limits on length of model... atomic and cg models can be built
   nastruct: ??? w/ arbitrary parameters and sequence?
   3DNA: I've used 3DNA to make very very long models and analyze them; NO
   CURVES: hard coded for ~150bp but SOURCE provided so recompiled as you see
   NASTRUCT: source? limits?

   On 05/26/2016 09:09 AM, Vlad Cojocaru wrote:

   Hi Tom,
   For Curves you also need a conversion to amber ASCII trajectories, so its
   also not perfect from that point of view .. I don't know how large and how
   many are your trajectories, but I did not see a major time limitation by
   having a temporary conversion to ASCII trajectories during an automated
   workflow that ultimately runs Curves on these ASCII mdcrd file (deleting
   them afterwords)...
   But, sure, I see the point that if cpptraj can do everything in one step, it
   will be more efficient .. Maybe I should also give it a try ....especially
   as Daniel mentioned it can actually do everything Curves does ....
   Best wishes

   On 05/26/2016 02:49 PM, Thomas C. Bishop wrote:

   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
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
   Thomas C. Bishop
    Tel: 318-257-5209
    Fax: 318-257-3823
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Received on Thu May 26 2016 - 12:30:05 PDT
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