Re: [AMBER] Pairwise Interaction Energy between two urea pairs

From: Jason Swails <>
Date: Fri, 12 Jun 2015 05:20:57 -0400

On Fri, Jun 12, 2015 at 2:45 AM, MOHD HOMAIDUR RAHMAN <>

> Dear Amber Users
> I am trying to calculate residue pairwise interaction energy between two
> urea molecules. For this I am using
> pairwise command likes this
> pairwise U0_U0 :URA out pairwise.dat cuteelec 0.0 cutevdw 0.0 avgout
> ura0_avgeout.dat eout ura0_eouttest.dat
> This command is calculating both inter and intra residue atom-atom pairwise
> interaction energy, While I need only inter residue pairs interaction
> energy.
> So how to calculate Inter residue pairs energy.

‚ÄčThe way I would do it is with 3 pairwise commands. In the first one you
select both urea molecules. In the second one you select the first urea
molecule. And in the third one you select the second urea molecule. The
intermolecular interactions should be the first energy less the sum of the
other two (i.e., just subtract off the intramolecular pairwise energies).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 12 2015 - 02:30:02 PDT
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