From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Thu Feb 12 2015 - 00:12:36 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/
>> >>
>> >>
>> >>
>> >>
>> >
>>
>>
>