Re: [AMBER] [cpptraj] Angle between atom and two centroids

From: Daniel Roe <>
Date: Fri, 18 May 2018 08:05:26 -0400


The 'angle' command can do this. Something like:

angle <domain1 mask> <linker atom mask> <domain2 mask> out angle.dat

Hope this helps,


On Fri, May 18, 2018 at 7:14 AM, Eiros Zamora, Juan
<> wrote:
> Dear cpptraj experts,
> I’m interested in calculating the ‘bending' angle of a protein that has two globular domains joined by a flexible linker.
> I think I can do this by defining a centroid for each globular domain (the center of mass) and calculate the angle formed by these two centroids to an atom located in the linker that joins them.
> Can this be done in cpptraj? If so, could you point me towards the relevant commands?
> Thanks,
> Juan
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Received on Fri May 18 2018 - 05:30:03 PDT
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