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

From: MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
Date: Fri, 12 Jun 2015 17:45:32 +0530

I have total 100 urea molecules and that is main issue to do this.

Suggest me how to proceed this.

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*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785*
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On Fri, Jun 12, 2015 at 2:50 PM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Fri, Jun 12, 2015 at 2:45 AM, MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com
> >
> wrote:
>
> > 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).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Fri Jun 12 2015 - 05:30:02 PDT
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