VMD-L Mailing List

From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Tue Feb 10 2015 - 22:35:48 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
Dear John Stone,

Thanks for the reply. The curly braces provided will take care of the
spaces in tcl scripting. I repeated by removing the spaces anyway, but
error remains the same. Is there any syntax error in the way namdenergy
command line which doesn't allow the plugin to recognize the directory?

Viswanath.
> 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/