From: Fotis Baltoumas (
Date: Mon Feb 09 2015 - 06:53:41 CST


This doesn't have to do with the location of your files per se. This error
means that your force field files do not contain parameters for at least
one atom in your system (the one named CR).
Check the parameter files you use and your structure. Either there is an
error in your structure files (an atom was misnamed in the psf&pdb,
therefore NAMD can't find it in the parameters) or you need parameters
that are not included in the force field files you use.
If your system does contain atoms not present in you "ILnWater.params"
file, find and include a parameter file that contains them. Note that the
"-par" option in NAMDEnergy can take more than one arguments, therefore
you could use multiple parameter files, for example:


> Hi,
> I'm trying to use NAMDEnergy plugin using following script. The directory
> of NAMD executable is located in environment variable "PATH". However,
> since it is not able to locate, I entered the path in the script with -exe
> flag. Still the plugin failed to locate the executable and prompted to
> specify the path. On specifying the path, the NAMD started to work but the
> plugin failed to locate the required Parameter file, with giving an error
> namd-temp.log. But these files are existing in the mentioned directory.
> What is the error that doesn't allow the plugin to locate the supporting
> files?
> package require namdenergy
> set OutFile Cs-CET
> set sel1 [atomselect top "name Cs1 and resid 1"]
> set sel2 [atomselect top "resname CET and resid 6"]
> set SwitchDist 10.5
> set Cutoff 12.0
> set ParamsFile {F:/Input Files/Analysis/{BMIM}{Tf2N}/IL219-DB18C6/NAMD
> Energy/ILnWater.params}
> set XSCFile {F:/Input Files/Analysis/{BMIM}{Tf2N}/IL219-DB18C6/NAMD
> Energy/IL219-Mixed_eq.xsc}
> set NAMDDIR {F:/Input Files/Analysis/{BMIM}{Tf2N}/IL219-DB18C6/NAMD
> Energy}
> namdenergy (-vdw || -elec || -nonb) -sel $sel1 $sel2 -ofile $OutFile
> -switch $SwitchDist -cutoff $Cutoff -par $ParamsFile -extsys $XSCFile -exe
> OS: Windows 8.1
> VMD Version: 1.9.2
> Thanks,
> Viswanath.