Re: [AMBER] Hydrogen bond analysis

From: David A Case <>
Date: Tue, 5 Aug 2014 08:50:30 -0700

On Tue, Aug 05, 2014, menwer momo wrote:
> I used ptraj for hydrogen bond analysis.

cpptraj is lots better than ptraj for this.

> The distance given in the output file, does it represent the hydrogen
> bond length or the distance between acceptor and receptor atoms ? 

I don't understand the distinction you are trying to draw: different people
will define the term "hydrogen bond length" in different ways. Beyond that,
in ptraj there are two "acceptor" atoms, and one "donor".

But it's easy for you to figure this out for yourself: do a "one-frame"
calculation, and compare the distance ptraj prints out with the actual
distance in the structure. This is the only way that you can be sure you
understand what ptraj is doing.

....good luck...dac

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Received on Tue Aug 05 2014 - 09:00:02 PDT
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