Re: [AMBER] Total interaction energy between monomeric units of a dimer

From: Hector A. Baldoni <>
Date: Thu, 20 Aug 2015 10:21:15 -0300 (ARGSL-ST)

Hi Jason,

I full agree, the attached files are meant just to learn.


> On Thu, 2015-08-20 at 09:09 -0300, Hector A. Baldoni wrote:
>> Hi Anu,
>> Attached you will find some in/out files about how to calculate the
>> interaction energies between protein-K+ using anal. You could download
>> anal software, compile and learn from the attached file how to use it.
>> I hope this will help you.
> But this does not address Dave's points about the lack of pairwise
> decomposability of the GB and PME potential energy functions.
> Sure, anal will give you something it *calls* an interaction energy, but
> that interaction energy will be a simple, gas-phase (maybe with an
> aphysical, distance-dependent dielectric) interaction that bears little
> resemblance to the potential energy function you actually run
> simulations with these days.
> In particular, the interaction between surface atoms of the two species
> is treated exactly the same as the interaction between two buried atoms
> near the interface. In a solvated environment, this is clearly the
> wrong thing to do if what you are interested in is the interaction
> energy in solution.
> The challenge here is that the GB and PME potentials -- which account
> for solvation effects in a more physically sensible model -- are not
> pairwise decomposable, so the anal approach will not work here. You
> need something different.
> For GB, the "pairwise decomposition" coded in sander treats the
> effective GB radii as a "constant" derived from the calculated effective
> radii of the entire system (when in reality the radii differ between the
> "bound" and "unbound" complexes). This approximation makes the GB
> potential pairwise decomposable. While approximate, it is almost
> certainly better than what anal does.
> For PME, the reciprocal sum is definitely not pairwise decomposable, and
> pair interaction energies need to be calculated by performing 3 separate
> nonbonded energy calculations -- one with the full system, one in which
> only the first part of the pair has nonzero nonbonded terms, and one in
> which only the second part of the pair has nonzero nonbonded terms. You
> still get contributions from the periodic images, so it's still an
> approximation, but it's significantly better than what anal did.
> I'd not suggest using anal for this purpose. The idecomp=3/4 option in
> sander and the 3-calculation PME approach are substantially better, and
> may give results that are even qualitatively different from what anal
> gives.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

 Dr. Hector A. Baldoni
 Area de Quimica General e Inorganica
 Universidad Nacional de San Luis
 Chacabuco 917 (D5700BWS)
 San Luis - Argentina
 hbaldoni at unsl dot edu dot ar
 Tel.:+54-(0)266-4520300 ext. 6157

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Received on Thu Aug 20 2015 - 06:30:05 PDT
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