Calculate energy of a residue using NAMD energy

From: Monika Madhavi (
Date: Mon Jan 29 2018 - 21:22:19 CST

Dear all,

I want to calculate the total energy of a specific residue (a water
molecule) at each frame. It is suggested that this can be done using NAMD
energy plugin. However, I would like to do the job through a script because
my trajectory is in a remote server.

I tried the following.
obtained the code in this link and created a .tcl file called
namdenergy.tcl in the folder where I have my script.

Then I wrote a different tcl script with
source namdenergy.tcl
namd energy -all -sel $sel -par myparameterfile.inp

Here I specified the parameter file because my parameter file is different
from the common charmm parameter file. However, I am getting the following

invalid command name "::FinderTool::find"

I would be grateful for a guidence to correctly use the namd energy to
calculate energies of some selected atomselections.

Thank you.

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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