AMBER Archive (2006)

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

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Fri Dec 01 2006 - 13:01:25 CST

Thanks a lot for your reply and help! I got it.
 One more thing I don't understand. What does it mean of "series" command? If I add it, it seems need more memory. Thanks!

Thomas Cheatham <tec3_at_utah.edu> wrote:
> 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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Esther B.

 
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