Re: [AMBER] Hydrogen Bond Occupancy

From: David A Case <>
Date: Tue, 22 May 2018 20:46:00 -0400

On Tue, May 22, 2018, Jerrano Bowleg wrote:

> I would like to perform a hydrogen bond analysis to identify the hydrogen
> bond occupancies for each guanine tetrad in G-quadruplex DNA. I have
> already performed MD simulation of 100 ns and I would to get the
> occupancies of each tetrad over the last 50 ns of simulation.

Have you tried the "hbond" action in cpptraj? It's very flexible,
albeit complex--it takes three pages in the manual just to describe the
options. But it's quite straightforward for a case like yours, where
you know which hydrogen bonds you want to follow.


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Received on Tue May 22 2018 - 18:00:03 PDT
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