From: Paweł Kędzierski (
Date: Thu Mar 28 2013 - 19:23:45 CDT

W dniu 28.03.2013 17:13, Mayne, Christopher G pisze:
> Pawel,
> Thanks for the patch! I had already applied a similar modification to the regex in our CVS some time ago, after other users had reported this error on VMD-L. This means that the fix should appear in the latest alpha builds of VMD 1.9.2 available through BioCoRE. However, if you send us the originally offending file, we can test against the latest version to ensure that the currently implemented patch functions as intended.
I had sent that file to as suggested by John Stone;
however, as it was calculated by the troublesome version 09RevC.01 of
Gaussian, I made these files for all steps from the initial optimization
up to the hessian for optimization of bonded parameters. You can
download them from
I have just downloaded vmd1.9.2a20 from BioCore and I see quite a few
differences in relevant plugins compared to what I used with vmd1.9.1.
Suddenly, errors disappeared. Good. Apparently, all these logs from C.01
are parsed without problems now.
There is only one minor glitch - gaussian does not like the ModRedundant
line "O * * * * R" saved by fftk in the hessian input file.

> With regard to the hessian, another user has reported problems with ffTK reading gaussian log files for the hessian calculation when using G09RevC.01. I was never able to track down the error as the user stopped replying and I don't have access to G09RevC.01 to test/track it myself. If you have access to G09RevB.01, the resulting log file should play nice with ffTK. To the best of my knowledge (I use ffTK almost daily), the latest VMD 1.9.2.alpha in combination with G09RevB.01 functions properly from start to finish.
Thanks, fortunately I have access to G09RevB.01.
Now I came up with more questions and comments.

 1. "QM Target Data" at "Opt. Charges" tab used to require two log files
    with single point energies for the compound and water (now three
    with MP2).
    It would be useful though to have an input field to directly provide
    the number for the energy instead of the file. First, because it
    would save two gaussian calculations (and possible problems with
    file parsing :-). The energy of the compound is already in the
    gaussian log file from optimization (both HF and MP2), and the
    HF/6-31G* energy of TIP3 water is always the same.
    Second, and the more important comment is that this implies that the
    interaction energies are calculated with basis set superposition
    error. This approach may agree with general CHARMM methodology but
    it would be interesting to check how it works with counterpoise
    corrected energies. Simple text fields for the energies of separate
    molecules would allow for such tests without the hassle of parsing
    gaussian log files from counterpoise calculations. It might e.g.
    turn out, that the scaling factor from gas to condensed phase would
    be more consistent with CP corrected interaction energies.
 2. In the new fftk version (from VMD 1.9.2a20) there are two entries
    for "Cmpd LOG" for optimization of charges: HF and MP2. What is the
    reason of providing MP2 energies for the compound only and not for
    water? Without this file, it doesn't run at all now - shouldn't it
    be optional?
 3. Apparently optimization for such simple molecule as H2S triggers a
    bug in namd2.8 which I had in path - the gradients are "nan" and
    namd allocates more and more memory until it gets killed (with vmd
    and fftk). I had a copy of ancient namd2.5 and this one worked. This
    is observed at optimization of bond and angle parameters.


> Regards,
> Christopher Mayne
> On Mar 28, 2013, at 9:34 AM, John Stone wrote:
>> Pawel,
>> 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!
>> Cheers,
>> 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
>> --
>> 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