Re: AMBER: H-bonds of peptide with water

From: Scott Pendley <>
Date: Mon, 7 Aug 2006 13:56:04 -0600


It would be helpful to know the question you are trying to answer but
lacking that try this . . . I have attached two generic ptraj files. You
don't want to have water as a donor and an acceptor in the same file,
otherwise all the water-water interactions will be calculated and things
will quickly get ugly.


P.S> This file looks for specific waters by name if you want to know water
interactions in general without residues numbers let me know and I will
provide you scripts to do that as well.

On 8/4/06, sangeeta <> wrote:
> Dear Amber Community,
> I am trying to analyse h-bonds formed between atoms of peptide and water
> during MD trajectory. When I run the Ptraj script attached herewith, I get
> only the intramolecular H-bonds in the peptide. No peptide-solvent H-bonds
> are reported in the output (also attached here). I would appreciate help
> reg. this. Is my script wrong somewhere? (It is a modified version of the
> script available in Amber Tutorial 8).
> Thanks.
> Sangeeta
> --
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Received on Wed Aug 09 2006 - 06:07:08 PDT
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