Re: [AMBER] Help on

From: Kenneth Huang <>
Date: Mon, 9 Jul 2018 17:20:08 +0000


You could try to use measuring the distance in cpptraj if you know a fixed reference point that you can measure the aspartate distance to and see how it changes with time.

You could also look at the waters around it, ie watershell, if your residue is becoming buried in the membrane, but that might be trickier to interpret if there happens to be enough water around in both positions.



From: Elisa Pieri <>
Sent: Monday, July 9, 2018 9:12 AM
To: AMBER Mailing List
Subject: [AMBER] Help on

Hello everyone,

I'm running a simulation of a protein in membrane (explicit solvent). I
have a ASP residue that is located at the frontier between water and
membrane, and it is dynamically flipping from being embedded in the
membrane and facing the water. I would like to plot this property against
the time coordinate. Since I have no MM analysis background on this topic,
could you tell me what kind of analysis should/could I run (presumably with

Sorry for this trivial question..could you help me?

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Received on Mon Jul 09 2018 - 10:30:02 PDT
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