From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Wed Feb 11 2015 - 00:55:18 CST

> In the log at the output you can see the parameter file was read. As
> mentioned earlier the error is with the parameters of the atom type not
> being found in the file. You said you ran the simulations, were they on
> the
> same system with the same parameter files.
Yes, the simulation was run with the same system and same input files
(PSF, Parameter including). I repeated the NAMDEnergy calculation by
removing the parameter file from the provided location. The namd-temp.log
files obtained from the calculations with and without providing parameter
file are identical returning same error. It means the plugin is not
accessing the parameter file at all. However, the calculation using GUI of
NAMDEnergy plugin works absolutely fine, but I prefer scripting. Or
otherwise, is it possible to generate tcl script from NAMDEnergy GUI with
preferences entered in it?

> On Feb 11, 2015 5:46 PM, "Viswanath Pasumarthi"
> <v.pasumarthi_at_iitg.ernet.in>
> wrote:
>
>> > 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/
>>
>>
>>
>>
>