Hi,
You can do this with cpptraj using the 'vector' command with two atom
masks, each of which correspond to one end of your alpha helix. The
backbone of the residues at each end of the helix is one potential
choice. You could then write a pseudo-trajectory using 'writedata' and
the 'vectraj' keyword if you want. You can also use the 'vectormath'
command to calculate the angle with another set of vectors (or a
single vector if you use the beta GitHub version). So e.g.
parm myparm.parm7
trajin mytraj.nc
vector H1 <mask0> <mask1>
writedata vector.H1.mol2 vectraj H1 trajfmt mol2
See the manual for more details. Hope this helps, at least to get started.
-Dan
On Sat, Feb 27, 2016 at 8:50 AM, Emilio Angelina
<emilioluisangelina.hotmail.com> wrote:
> Dear Amber users,
>
> I wonder I there is a way of drawing a vector along the axis of an alpha helix with ptraj or cpptraj so that I can then follow the angle formed between this vector along the trajectory, with some other vector in a reference structure.
>
> Thanks in advance
> Emilio
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 27 2016 - 13:00:04 PST
