VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
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
./../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.
-- 
Best,
/A