Hi,
In the cpptraj part of the Amber 14 manual there is a section entitled
'28.14 Matrix and Vector Analysis', which includes a command called
'vectormath'; 'vectormath dotangle' should get you what you want.
-Dan
On Wed, Mar 11, 2015 at 2:01 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> Dear Sir,
>
> I would like to calculate an angle between two chains of a lipid. For
> example lets say I have a lipid:
>
> C70
> C
> C
> C
> C63
> (headgroup)---/
> \
> C52
> C
> C
> C62
>
> I want to calculate the angle in between the two chains. So I try to define
> a vector along atos C63--C70 and C52--C62. The cpptra code I wrote is a
> below:
>
> cpptraj topology << EOF
> trajin trajectory.nc
>
> vector v1 :1.C52 :1.C62
> vector v2 :1.C52 :1.C70
>
> ?? WHAT COMMAND to calculate the angle ??
>
> EOF
>
> I wish to get some help to know the suitable command to calculate the
> angle between these vectors.
>
> Many thanks in advance.
> Regards
> Vijay
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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 Wed Mar 11 2015 - 08:00:07 PDT
