# Re: [AMBER] calculating angle between to vectors

From: Vijay Achari <glycoamber.gmail.com>
Date: Thu, 12 Mar 2015 13:22:45 +0800

Dear Dan,

I used the script below and I got the angles.

cpptraj \$top <<EOF
trajin \$path/reImaged-bcmLyo25perR.nc 15001 60000

vector v1 :\$i.C52 :\$i.C62
vector v2 :\$i.C52 :\$i.C70

vectormath vec1 v1 vec2 v2 out vector-Test-lipid-\$i.dat name chainAngle
dotangle

EOF

Regards

On Wed, Mar 11, 2015 at 10:39 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> 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
> > \
> > 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
> > _______________________________________________
> > 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
>
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Received on Wed Mar 11 2015 - 22:30:03 PDT
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