From: Prof. Eddie (
Date: Fri Jun 14 2013 - 11:45:14 CDT

Hello all,
I would like to look at the non-bonded interaction of two residues (part of
a catalytic triad) using the namdenergy plugin. I can do
this successfully (at least I obtain numbers). My problem is I clearly do
not understand what is being calculated.

When I use the selection (on command line) -sel "residue 138" "reside 56" I
get the electrostatic and VdW energies. My protein is protinated yet my
electrostatic interaction is huge (~ 25 kcal/mol) which is not possible for
neutral residues (Ser and His). The VdW interaction is of the right order.

Since both residues are protinated, what is namdEnergy calculating for the
electrostatic energy to be so high?

Further, when you select a residue and the protein does it chop off at the
CA and thus give the energy including the CA-C bond of the residue? Or does
it remove the residue from the backbone in which case it counts the bonds
on the backbone? If I only chose two atoms on different residues will the
energies be only their interaction as if they were not bonded in their won
respective residues or is it truly the residual interaction between those

Basically, how does namdenergy segment the system for different selections.

Edward Ackad, Ph.D <>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390