From: Viswanath Pasumarthi (
Date: Mon Feb 09 2015 - 07:59:09 CST

> Hello,
> 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:
> Fotis

Mr. Fotis,

Sorry for not mentioning this earlier, I did cross check that before
posting. These were the same input files used to perform the simulation
>> 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.