From: John Stone (
Date: Thu Mar 28 2013 - 09:34:50 CDT

  Can you also send us the Gaussian log file that goes with the patch?
It is helpful for us to have a collection of log files that previously
encountered trouble with parsers, so we can re-test them when changes
are made to the code. No need to send it to VMD-L, just email a gzipped
log file to, or if it is too large, then post it somewhere
and send us a URL. Thanks!

  John Stone

On Thu, Mar 28, 2013 at 03:25:50PM +0100, Pawe?? K??dzierski wrote:
> Dear Christopher,
> Thank you for prompt answer.
> W dniu 28.03.2013 14:03, Mayne, Christopher G pisze:
> >Updates of geometry (PDB file) and charge (PSF file) are done directly in
> >their respective tabs. The "Update Parameter File with Optimized
> >Parameters" is only used when updating bonds, angles, and dihedrals, after
> >optimization. Note that the "Optimization LOG File" required there is the
> >log file written by ffTK, which contains a portion at the end denoted by
> >"FINAL PARAMETERS" tag, NOT a Gaussian log file.
> Ooops, I missed this detail, sorry.
> In the mean time I have progressed a bit but now I am getting errors
> parsing Gaussian log files from QMtool.
> I know that Gaussian people are often playing tricks with their log
> files as I have my own script parsers which break from one version to
> another. And I already found one such bug (patch attached) but now I
> have problems with hessian parser which seem more involved.
> Could you advice which version of Gaussian is recommended/best tested
> with FFTK and the plugins it depends on? I have some choice at our
> computing center and I would like first make myself familiar with fftk
> rather than chasing parsing bugs without good understanding of tcl.
> >I strongly suggest viewing the screencasts available on the documentation
> >page:
> I did. I just need to get thorough the tricky details. BTW, you did an
> excellent piece of work.
> Greetings,
> Pawel
> >Christopher Mayne
> >
> >
> >On Mar 28, 2013, at 6:26 AM, Pawe?? K??dzierski wrote:
> >
> >>Dear all,
> >>I have just started playing with FFTK, and want to make sure that I get
> >>it correctly.
> >>As a simple test case I started with H2S molecule and got successfully
> >>through most of BuildPar tab; that is, I have assigned LJ parameters and
> >>saved optimized geometry as PDB. I checked that the numbers and coords
> >>are correct in par and pdb files.
> >>So far, it means that basic parsing of gausian log file works.
> >>Now I got to the "Update Parameter File with Optimized Parameters" part.
> >>When I load the "Optimization LOG File:" and then click the "Write
> >>Updated Parameter File" button, the par file is updated (checked by
> >>modification time" but the equlibrium parameters (b0 and Theta0) are
> >>saved as zeros.
> >>Is this expected behaviour? Or may it be that the plugin is incompatible
> >>with gaussian 2003 (g03) which I use?
> >>Thank you in advance,
> >>Pawel
> >>

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