From: Ashar Malik (
Date: Thu Feb 12 2015 - 00:48:48 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
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