Re: [AMBER] neighbouring protons

From: Jason Swails <>
Date: Tue, 10 Nov 2015 07:32:34 -0500

On Tue, Nov 10, 2015 at 4:59 AM, Neha Gandhi <> wrote:

> I want to figure out list of neighboring protons near a specific atom
> (within 5 Angstroms) encountered during trajectory. How can I achieve this
> using cpptraj?
> Your feedback is appreciated.

​You can use the "mask" command with a distance-based mask selection.
Here's a brief description of distance-based masks:

Note, this will just tell you *which* atoms meet the criteria each frame,
it won't tell you the distances. Also, "mask" is the only command in
cpptraj in which the mask is evaluated for each frame (for every other
action, the mask is evaluated once on the first or reference frame).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 10 2015 - 05:00:03 PST
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