Re: [AMBER] when nastruct does NOT print the basepair information

From: Daniel Roe <>
Date: Thu, 15 May 2014 09:25:38 -0600

The 'nastruct' command determines base pairing from the first frame or
a given reference frame. It then uses that information for the rest of
the run; this is done to simplify book-keeping. When the [hb] field
goes to zero, nastruct will still try to calculate BP parameters. In
the future it might be useful for there to be an option to prevent
calculation of BP parameters after the base pair breaks, but that is
not currently implemented.


On Thu, May 15, 2014 at 8:52 AM, newamber list <> wrote:
> HI All
> I am using cpptraj 'nastruct' option with AT14. I have starting 15 base
> pairs so during evolution of MD some base pairs breaks as expected. In
> comparison to my initial pairs finally I get 13 basepairs as calculated by
> nastruct.
> I am wondering when nastruct does NOT print the basepair information? Is it
> when H-bonds between base pairs goes zero then base pair info is not
> printed (as manual says at least one H bond should be present) or some
> other factor among the Shear, Stretch, Stagger, Buckle, Propeller, Opening.
> If not then I would expect it should print H-bond being '0' or it simply
> ignores printing them.
> thanks
> JIom
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Thu May 15 2014 - 08:30:03 PDT
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