just add a tiny comment to Dan's one:
need to add "groovecalc 3dna" to "nastruct" command to reproduce groove
width in 3DNA.
Hai
On Thu, May 26, 2016 at 9:16 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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
> determined.
>
> On Wed, May 25, 2016 at 5:31 PM, Thomas C. Bishop <bishop.latech.edu>
> 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>
> run
> 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
> conformations.
>
> Let me know if you have any more questions. Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Thu May 26 2016 - 07:00:02 PDT
