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