Re: AMBER: H-bond analysis (Ptraj)

From: Thomas Cheatham <>
Date: Fri, 1 Dec 2006 11:00:05 -0700 (Mountain Standard Time)

> I use the Ptraj to do the Hbond analysis, when I run it, it says:
> HBOND output to file output_hbond1.dat,
> data will be sorted, intra-residue interactions will NOT be included,
> ...........
> I only calculate in the same residue (MIC), I don't know why it doesn't
> calcuate the Intra-residue interactions.

Add the "includeself" keyword

hbond series h1 out hbond.dat includeself

[INTRA-residue self interactions are omitted by default since these
clutter up the display and in many cases are not meaningful.]


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Received on Sun Dec 03 2006 - 06:07:55 PST
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