VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 09 2015 - 11:12:35 CST

Hi,
  I noticed that some of the paths shown in your output appeared to
have directory names containing spaces. Try renaming those directories
so they don't contain spaces and see if that cures your problem.
Many applications and/or scripts that were originally developed on Unix
(and NAMD is a likely case) don't like file or directory or path names
that contain spaces. I would suggest trying a short work directory name
like "f:/namdenergytest" with no spaces, and see if that works.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 09, 2015 at 07:29:09PM +0530, Viswanath Pasumarthi wrote:
>
>
> > 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
> successfully.
> >
> >
> >> 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.
> >>
> >>
> >
> >
> > 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/