Hi,
I'm CCing my reply to the Amber mailing list in case other people have
encountered this issue.
On Tue, Feb 11, 2014 at 2:18 PM, Mei Liu <judyliu317.gmail.com> wrote:
> Today i have get some files when i used the key word "nastruct" to deal
> with the DNA trajectory without any major and minor groove information.
> (BP. and BPstep. and Helix.)
>
> I read AmberTools 13 manual which said i will get the major and minor
> information.
> But i do not know why?
>
The data is actually calculated (you can see this in the 'DATASETS:' part
of the output), but I never added it to the output of the 'nastruct'
command (this will be fixed in the next release). You can however create a
file for the data like so:
parm asu_nobox.prmtop
trajin 01_01_nobox_100.trj
nastruct naout nastruct1.dat resrange 1-20
run
write MajorMinor.dat NA_00000[major] NA_00000[minor]
The file 'MajorMinor.dat' will contain major groove data for each base pair
followed by minor groove data for each base pair in columns like so:
#Frame 1G16C 2G15C 3G14C 4C13G 5G12C ... 1G16C ...
1 0.000 18.600 18.778 20.351 19.961 ... 13.329 ...
2 0.000 18.829 19.093 19.568 19.295 ... 13.320 ...
3 0.000 18.168 18.774 19.966 19.787 ... 13.341 ...
The 'NA_00000' data set name is the default one used by 'nastruct' when
none is provided. If you named the 'nastruct' data (e.g. 'DNA') you would
use that name instead, e.g.
nastruct naout nastruct1.dat resrange 1-20 DNA
run
write MajorMinor.dat DNA[major] DNA[minor]
For the 'write' command you can change the file format by changing the
extension, e.g. MajorMinor.agr for grace or MajorMinor.gnu for gnuplot.
Hope this helps; let me know if you have any more questions.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 12 2014 - 08:00:03 PST
