From: Viswanath Pasumarthi (
Date: Thu Feb 12 2015 - 02:58:11 CST

> after reviewing all your posts and the script you attached at the
> beginning
> here is something:
> look at the following snippet of my script that works perfectly fine for
> me
> ---
> namdenergy -nonb -sel [atomselect top "segname N1 and resid $rid_"]
> [atomselect top "protein"] -norun -extsys ../../equil_npt.xsc -pme -par
> ../../par_all36_prot.prm -par ../../par_all36_na.prm -par
> ../../toppar_water_ions.str
> notice that I pass MULTIPLE files -- the "PROBLEM" is in the way you are
> putting it together - and NOT with the program.
> Instead of persisting with the way you are providing the -par with the
> location of your files, you can clearly see that it is NOT working for you
> -- try stating the paths DIRECTLY -- and as stated before try removing the
> spaces. Since you are working with windows it wont hurt for trial to MOVE
> the files to a location that you can access easily for a trial run and
> trouble shoot this problem, NOW that you know that the files that you are
> TRYING to read are NOT being READ and instead the NAMDenergy plugin is
> using DEFAULTS.

Thanks Ashir for your inputs,
I have copied the files into another directory with no spaces in its path
(F:/Dropbox/NAMDEnergy). And, repeated the calculation by stating the
paths 'directly', as follows:

package require namdenergy
namdenergy (-vdw || -elec || -nonb) -sel [atomselect top "name Cs1 and
resid 1"] [atomselect top "resname CET and resid 6"] -extsys
IL219-Mixed_eq.xsc -par ILnWater.params

Another attempt by moving the supporting files a folder up:
package require namdenergy
namdenergy (-vdw || -elec || -nonb) -sel [atomselect top "name Cs1 and
resid 1"] [atomselect top "resname CET and resid 6"] -extsys
./IL219-Mixed_eq.xsc -par ../ILnWater.params

NAMDEnergy is identifying the selections between which interaction
energies need to be calculated, but the flags -extsys, -par, -exe,
-cutoff, -switch are not being read when included in the command line.
This is evident when it writes the namd-temp.namd file where it fails to
include these data which it failed to read. So, running the calculation
using this configuration file results in the error of missing parameters.