Re: [AMBER] Angle calculation between two structures

From: Daniel Roe <>
Date: Fri, 15 Jan 2016 08:59:52 -0700


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:

vector V1 corrplane <mask1>
vector V2 corrplane <mask2>
vectormath vec1 V1 vec2 V2 dotangle out angleV1V2.dat

Hope this helps,


On Fri, Jan 15, 2016 at 5:58 AM, anu chandra <> 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
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jan 15 2016 - 08:30:03 PST
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