Re: [AMBER] angle of domain movement calculation

From: Carlos Simmerling <>
Date: Wed, 23 Aug 2017 11:58:53 -0400

Ptraj and cpptraj can do this using distance or angle calculations, perhaps
with centers of mass. This is described in the manual. However, the details
of which atoms to use are really something that you'll need to determine
yourself. You need to analyze your trajectory and choose groups of atoms
that are best to quantify this motion. That is different for each system
and will be part of the research you need to do.

On Aug 23, 2017 6:06 AM, "sangita kachhap" <> wrote:

> Dear Amber developer
> I have done 75ns MD simulation of a metalloprotein. During trajectory
> visualization, I have observed the domain motion resulting in opening of
> the active site.
> So now I want to calculate the angle of domain movement.
> Please suggest how to perform it using ptraj/cpptraj.
> Thanks
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Received on Wed Aug 23 2017 - 09:00:04 PDT
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