Re: [AMBER] MMPBSA Energy between system and its image

From: Ahmed Ayoub <>
Date: Fri, 4 Jul 2014 15:15:44 -0600

Hi Jason,

Thanks for your help. I just want to make sure of something. Do you have an
easy way of creating the topology files for the two subunit system? I'm
thinking of replicating the system using, maybe, PropPDBmodule and taking
it to tleap. Is that fine?

Also the processing of the trajectory to contain only the two images I'm
interested in; do you know of an easy way yo do it? Is there a way in ptraj
I can do it?


> Message: 5
> Date: Thu, 3 Jul 2014 13:02:20 -0700
> From: Jason Swails <>
> Subject: Re: [AMBER] MMPBSA Energy between system and its image
> To: AMBER Mailing List <>
> Message-ID: <>
> Content-Type: text/plain; charset=us-ascii
> On Jul 3, 2014, at 12:41 PM, Ahmed Ayoub <> wrote:
> > Dear amber users,
> >
> > I have a system which contains a protein subunit but using PBC, I'm
> > effectively simulating a thread of infinite length of this subunit.
> > However, I want to use the MM/PBSA to calculate the energy of interaction
> > between the system and one of its adjacent PBC image. Is that possible?
> Maybe. You'll have to create a new topology with your original protein
> subunit and the one extra periodic image whose energy you want to
> calculate. Then you need to process your trajectory and create a _new_ set
> of coordinates with just the 2 images of the protein subunit you want to
> analyze (and nothing else -- it needs to match your new prmtop file). Then
> you can use MM/PBSA or MM/GBSA to analyze the energies -- you would
> basically analyze the energies of an isolated subunit and subtract double
> that number from the energy of the larger system with the 2 periodic images.
> There are no tools that can automate any of those tasks (except
> for the last part). It would be _much_ easier to compute the interaction
> energy without an implicit solvent model between a single subunit and all
> of its periodic images. But these are fundamentally different
> calculations, since the former includes the effects of solvent screening of
> the electrostatic interactions whereas the latter would not. It all
> depends on what exactly you want to compute.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> ------------------------------

Ahmed Taha Ayoub
PhD Candidate, Theoretical and Computational Chemistry
W4-54, Department of Chemistry
11227 Saskatchewan Drive
University of Alberta
Edmonton, Alberta T6G 2G2
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Received on Fri Jul 04 2014 - 14:30:03 PDT
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