From: Mayne, Christopher G (
Date: Tue Aug 18 2015 - 15:58:35 CDT

We have very much deprecated Paratool in favor of ffTK; however, we've tried to keep QMTool as functional as possible. It appears that the error is occurring in the QMTool parser. If you send your PSF, PDB and Gaussian IO files I'll take a look to try and figure out where the parser is choking.


Christopher Mayne

On Aug 18, 2015, at 1:09 PM, Prof. Eddie wrote:

I am using paratool for a first pass before fftk (in the end I want to build a course grain model so my parameter's need not be perfect). I fixed the problem with g09 and now it does converge, but I still get the same error parsing the file.

I can modify the qm_tool.tcl files to fix the problem (at least this problem, then another comes up). Is paratool really completely deprecated and can't parse g09 files anymore? Or are there patches somewhere I can use?

On Mon, Aug 17, 2015 at 11:09 PM, John Stone <<>> wrote:
  Paratool has been (greatly) superceded by ffTK in recent versions of VMD,
so if you're developing parameters I would suggest using ffTK instead.
If you're doing something else (e.g. only using qmtool and not paratool)
maybe you could provide more commentary on this and someone might be able
to make a helpful suggestion. My assumption from the errors you provided
below is that there are issues with parsing the output from g09 which
terminates subsequent processing after that point.

  John Stone<>

On Mon, Aug 17, 2015 at 02:52:20PM -0500, Prof. Eddie wrote:
> Hello,
> I'm trying to import the charges calculated via the Hessian (from paratools
> Qm gui). I keep getting the error:
> invalid bareword "Sum"
> in expression "Sum-1";
> should be "$Sum" or "{Sum}" or "Sum(...)" or ...
> invalid bareword "Sum"
> in expression "Sum-1";
> should be "$Sum" or "{Sum}" or "Sum(...)" or ...
> (parsing expression "Sum-1")
> invoked from within
> "expr [lindex $line 0]-1"
> (procedure "read_gaussian_espcharges" line 30)
> invoked from within
> "read_gaussian_espcharges $fid"
> (procedure "read_gaussian_log" line 360)
> invoked from within
> "read_gaussian_log $file $molid"
> (procedure "load_gaussian_log" line 17)
> invoked from within
> "load_gaussian_log $file"
> (procedure "::QMtool::load_file" line 10)
> invoked from within
> "::QMtool::load_file $file [string range [file extension $file] 1 end]"
> (procedure "load_molecule" line 14)
> invoked from within
> "load_molecule SIP $file"
> (procedure "::Paratool::opendialog" line 131)
> invoked from within
> "::Paratool::opendialog loadsip "[file rootname
> ${::Paratool::molnamebase}]_sp""
> invoked from within
> ".paratool.#paratool#menu.#paratool#menu#hessian invoke active"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke active]"
> (procedure "tk::MenuInvoke" line 50)
> invoked from within
> "tk::MenuInvoke .paratool.#paratool#menu.#paratool#menu#hessian 1"
> (command bound to event)
> I know my convergence is not great since gaussian (09) gives:
> Item Value Threshold Converged?
> Maximum Force 0.000032 0.000450 YES
> RMS Force 0.000004 0.000300 YES
> Maximum Displacement 0.005351 0.001800 NO
> RMS Displacement 0.001625 0.001200 NO
> Predicted change in Energy=-3.071138D-08
> but I'm trying to make it better. In the meantime I would at least like to
> know how to fix the problem paratool is having parsing the file. I am using
> vmd 1.9.2 with gaussian09. Any ideas?
> Thanks
> Eddie
> --
> _________________________________________________________
> Edward Ackad, Ph.D <>>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390<tel:%28618%29%20650-2390>

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801>           Phone: 217-244-3349<tel:217-244-3349>>
Edward Ackad, Ph.D<>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390