VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Mon Feb 11 2013 - 08:51:38 CST

Hello all,
I would like to look at the non-bonded interaction of two residue (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?

Any ideas?
Thanks
Eddie 

-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390