Re: [AMBER] cpptraj + nastruct

From: Daniel Roe <>
Date: Thu, 26 May 2016 07:16:03 -0600


Glad to hear that 'nastruct' has been working for you - I'll answer
your original questions below. Under the hood, the 'nastruct' command
uses the same algorithms and base reference frames as 3DNA, so all
quantities calculated should match 3DNA exactly. The only thing that
cpptraj does not do is calculate global helical axis parameters -
however, local helical axis parameters for base pair steps are

On Wed, May 25, 2016 at 5:31 PM, Thomas C. Bishop <> wrote:
> I'm using CPPTRAJ to analyze some simulations w/ dsDNA and want to extract
> 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?

Currently you can't tell 'nastruct' which bases are paired (although
this is a good suggestion). The 'nastruct' command typically does a
decent job of determining base pairing (as of AT16 this includes
non-WC base pairs) and base pair steps. If you have a case where
'nastruct' is failing to determine a base pair let me know.

> Pointers to tools for statistically summaries of the results would be much
> appreciated.

The 'avg' analysis command can be used to get average, standard
deviation, etc for the various quantities that 'nastruct' determines.
For example:

nastruct MyData <more nastruct args>
runanalysis avg MyData[hrise] out Hrise.avg.dat

You can also process multiple sets at once by specifying "MyData[*]"
for example (see the manual for full details on data set selection).
You could also use the 'avg' command on previously generated data in a
separate cpptraj run via the 'readdata' command. You can also use the
'stat' analysis command on the pucker data sets (in this case named
'MyData[pucker]') to determine the populations of pucker

Let me know if you have any more questions. Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu May 26 2016 - 06:30:02 PDT
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