From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Mon Feb 09 2015 - 06:32:15 CST

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
"FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CR" in the
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
$NAMDDIR

OS: Windows 8.1
VMD Version: 1.9.2

Thanks,
Viswanath.