From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Wed Feb 11 2015 - 03:14:15 CST

> That's not the log I am referring to. I am referring to. The name energy
> is
> a two process thing ... One in which the DCD is manipulated with the
> selections generating a temp series of file including a config file which
> then runs and produces the energy values. The error you listed is in the
> second part. That log is the one which you will need to look at. The error
> is different in case the files are missing. If the -par is not used the
> plugin uses the files that are hardcoded. Gui does the same. I repeat the
> error is what is stated in the output. Missing parameters.
You may check temp files obtained for both cases here
(https://www.dropbox.com/sh/s68uehybne903gc/AACNVWH-lLKPKiJW0RU2wPj_a?dl=0).
It is true that parameters are missing. Missing because the plugin is
using the parameters that are hardcoded (the ones that are provided with
VMD installation), and not from the location I provided with -par flag in
the NAMDEnergy command line. That is whole point.

> On Feb 11, 2015 7:55 PM, "Viswanath Pasumarthi"
> <v.pasumarthi_at_iitg.ernet.in>
> wrote:
>
>> > 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/
>> >>
>> >>
>> >>
>> >>
>> >
>>
>>
>