Re: [AMBER] Angle calculation between two structures

From: anu chandra <anu80125.gmail.com>
Date: Fri, 15 Jan 2016 17:24:55 +0000

Hi Daniel,

Many thanks for your prompt reply. I just have a quick query here. In my
case, <mask1> in ' vector V1 corrplane <mask1> ' comes from the starting
structure of simulation and <mask2> in ' vector V2 corrplane <mask2> '
comes from each frame of the simulation trajectory. This means, every time
when the 'dotangle' is calculated the V1 remains constant (as the vector
comes from starting structure) and V2 get update from frame to frame. I
just wonder whether this can be possible with the steps you suggested.

Many thanks once again

Anu

On Fri, Jan 15, 2016 at 3:59 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> You could probably do what you want with 2 'vector corrplane' commands
> to get vectors normal to the planes defined by whatever atoms you
> want, then 'vectormath dotangle' to get the angle between them.
> Something like:
>
> vectormath vec1 V1 vec2 V2 dotangle out angleV1V2.dat
>
> Hope this helps,
>
> -Dan
>
> On Fri, Jan 15, 2016 at 5:58 AM, anu chandra <anu80125.gmail.com> wrote:
> > Dear Amber users,
> >
> > The protein I am working with have three domains. Now I am trying to
> > calculate a dihedral angle defined by two structures, the starting
> > structure and a snapshot from simulation trajectory. More precisely, a
> > plane is drawn between the center of mass of three domains, and the
> > dihedral angle of interest is formed by this plane from starting
> structure
> > and a simulation snapshot. I just wondering possibilities of doing such
> an
> > angle calculation with CPPTRAJ.
> >
> >
> > Any help is appreciated
> >
> > Anu
> > _______________________________________________
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> > 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)
>
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>
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Received on Fri Jan 15 2016 - 09:30:04 PST
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