[AMBER] RMS rotate about z-axis only

From: Wesley Michael Botello-Smith <wmsmith.uci.edu>
Date: Tue, 11 Sep 2018 13:02:49 -0700

Hello all,
 I am working on a project where I need to make measurements of membrane
geometry in the presence of a protein.
 The problem I am having is that when I attempt to align the protein using
the rms function in cpptraj (or pytraj) with the protein as a the reference
mask, it ends up tilting the membrane. This complicates some future
measurements I am doing.
 What I would like to be able to do is tell the rms function to only apply
rotations about the z-axis. I.e. only apply rotations that do not change
the z-coordinates of atoms. Does anyone know of a way to do this
efficiently within cpptraj (or pytraj)?
 If need be I can always do norotate and then manually perform the z-axis
rotation in python, but I would like to avoid re-inventing the wheel, so to
speak, if possible.

Thanks in advance,
-Dr. Wesley Botello-Smith
AMBER mailing list
Received on Tue Sep 11 2018 - 13:30:02 PDT
Custom Search