Thanks very much for your help!
Emilio
> Date: Sat, 27 Feb 2016 13:57:38 -0700
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] draw vector along axis of an alpha helix
>
> 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
> >
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>
>
>
> --
> -------------------------
> 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 Sat Feb 27 2016 - 14:00:04 PST
