From: Dr. Eddie (eackad_at_gmail.com)
Date: Mon Jun 17 2013 - 08:43:44 CDT
I would like to look at the non-bonded interaction of two residues
(part of a catalytic triad) using the namdenergy plugin for vmd. I can
do this successfully (at least I obtain numbers). My problem is I
clearly do not understand what is being calculated. I know this is not
a vmd list (I've tried the vmd list more than once and never got a
response) and this is more about namd since namdenergy just calls
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 atoms.
Basically, how does namdenergy (using namd) segment the system for
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