Re: [AMBER] pairwise command in cpptraj

From: Daniel Roe <>
Date: Tue, 5 Feb 2019 12:44:39 -0500


The pairwise command is available in cpptraj version 12. However,

1) Version 12 is several years out of date. I highly recommend you update.
2) The 'pairwise' command was really designed to look at single pairs
- doing each water molecule will require some scripting on your part.
3) The 'pairwise' command uses an extremely simple nonbonded model (no
cutoff, no periodicity), so the energies you obtain aren't going to
really match what the actual system would "feel". That's not to say
you can't get any useful information this way, but keep it in mind.
You may want to use a more sophisticated tool for water analysis
instead like GIST (available in later versions of cpptraj).


On Tue, Feb 5, 2019 at 7:38 AM Leena Aggarwal <> wrote:
> Dear Amber Users
> I want to calculate the pairwise interaction energy of each water molecule
> with the protein in water-protein system.
> I have AMBER 12 and I want to use the *pairwise command in cpptraj* which
> is available in latest versions of AMBER.
> Is there any solution so that I will be able to use pairwise command of
> cpptraj in AMBER 12.
> From
> Leena Aggarwal
> University of Delhi
> India
> _______________________________________________
> AMBER mailing list

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Received on Tue Feb 05 2019 - 10:00:03 PST
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