Hi Mariam,
I'm doing something similar at the moment. As Hai was saying, you can calculate vectors based on the distances between the centers of mass of your targets using the vector command in cpptraj. Once you have that, you can calculate the angle between them either directly in calc/excell/origin/your own script, or directly using the vectormath command in cpptraj. Just check both of them in the Amber 15 manual, they're pretty easy to use.
Manuel
-----Original message-----
From:maryam azimzadehirani <
maryamai1988.gmail.com>
To:AMBER Mailing List <amber.ambermd.org>
Date:Fri, 26 Feb 2016 15:20:57
Subject:[AMBER] the angle between two axis
Dear Amber users,
I want to calculate the angle between two axis which each of them is the
axes joining the centre of mass of two subdomains. I already looked for it
in the amber mailing list, I couldn’t find any posts. Can you advice me in
this regards.
thanks
Maryam
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Received on Fri Feb 26 2016 - 00:30:02 PST
