AMBER Archive (2006)

Subject: AMBER: angle between planes

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Fri Apr 07 2006 - 11:55:59 CDT

Dear All,

I would like to calculate the relative orientation between side chains of
opposite peptide strands. I believe that this can be done by defining a
plane for each side chain using 3 carbon atoms from each side chain and then
calculating the angle between the two planes by stepping through the
trajectory frames. Is it possible to do something like this with ptraj? The
"angle" function if I understand correctly calculates angles between 3 atoms
and I don’t think it would give a meaningful result for my problem.

Thank you very much for any advice.

Regards,

John 

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