Re: [AMBER] Query about residue decomposition energy

From: Kshatresh Dutta Dubey <>
Date: Fri, 22 Nov 2013 20:11:13 +0530

Dear Jason,

Thanks for such detail explanation. I have still a query; in biomolecular
systems, hydrogen bonds and salt bridges are assumed to be the strongest
non covalent interactions whose value are still less than 5-6 kcal/mol.
What will be the interpretation of this energy (~12 kcal/mol)? Another
point; I think that your given example (-332 kcal/mol) is for two
monovalent ions, not for the present case (two charged amino acids). My
issue is that, -12 kcal/mol looks fine if it is electrostatic interaction
only, but for free energy between two residues it still seems very large
(we have already compensated electrostatic energy with polar solvation


"That said, 12 kcal/mol is not at all unreasonable for an electrostatic
> interaction between charged species. Consider the basic electrostatic
> equation U=k*q1*q2/r. For 2 monovalent ions (of opposite charge)
> separated by 1 Angstrom, the energy is -332 kcal/mol. When separated by
> 10 Angstroms, the interaction energy is still -33 kcal/mol! You would
> need to separate 2 monovalent ions by almost 30 Angstroms to drop the
> interaction energy to 12 kcal/mol. Solvation effects temper this
> interaction, but their values are still large."
> The main point is that electrostatic energies are HUGE---by far the
> largest energies in just about any force field. Interaction energies
> like these can be qualitatively useful for some comparisons, but should
> be interpreted carefully.
> Energies in biomolecular systems are very frequently compensatory.
> Large electrostatic energies are frequently offset by solvation energies
> that are on the same order of magnitude, so that total energy changes
> are frequently relatively small. You will find this principle is
> pervasive throughout computational chemistry.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Nov 22 2013 - 07:00:03 PST
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