AMBER Archive (2006)

Subject: Re: AMBER: H-bond analysis (Ptraj)

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Fri Dec 01 2006 - 12:00:05 CST

> 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.]

--tom

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