AMBER Archive (2006)

Subject: Re: AMBER: H-bonds of peptide with water

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Mon Aug 07 2006 - 14:56:04 CDT

sangeeta,

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.

Scott

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 <sangeeta_at_bioinfo.ernet.in> 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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>
>



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