From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue Aug 18 2015 - 13:09:22 CDT

Hi,
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?
Thanks,
Eddie

On Mon, Aug 17, 2015 at 11:09 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> Paratool has been (greatly) superceded by ffTK in recent versions of VMD,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.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> 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 <http://www.siue.edu/%7Eeackad>
> > Assistant Professor of Physics
> > Computational Nanophotonics
> > Southern Illinois University Edwardsville
> > (618) 650-2390
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>

-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390