Re: [AMBER] Query about residue decomposition energy

From: Jason Swails <>
Date: Fri, 22 Nov 2013 07:51:30 -0500

On Fri, 2013-11-22 at 16:28 +0530, Kshatresh Dutta Dubey wrote:
> Dear all,
> I am using residue residue energy decomposition for protein-peptide complex
> using GB method,, Amber12. My GB variables are -
> &gb
> igb=5, saltcon=0.150,
> /
> For some residue pairs say, ASP-ARG, GLU-ARG, the total delta G is
> ~12.kcal/mol. Though, these are charged residues and may show large
> interaction energy but still ~12 kcal/mol for single residue pair seems to
> be very high. I am curious to know the validity of this energy value. I
> will deeply appreciate all suggestions.

Take decomposition results with a grain of salt. First of all, GB is
not strictly pairwise decomposable. This has been discussed extensively
on this list in the past. The main issue is that the effective GB radii
are functions of the local environment and therefore includes
contributions from all residues surrounding a particular residue. Thus,
residue C affects the interaction energies between residues A and B
through its contributions to the effective radii of the atoms in
residues A and B.

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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 22 2013 - 05:00:02 PST
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