VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Oct 28 2013 - 08:05:37 CDT

Shane,

Check BioCoRE for the VMD 1.9.2a35 builds posted on Oct. 24. These should have the appropriate updates.

Regards,
Christopher Mayne

On Oct 23, 2013, at 4:51 PM, Christopher Mayne wrote:

> Shane,
>
> Thanks for sending me the files offline. As I suspected, I was able to track the errors down to changes to the Gaussian log file and made the necessary fixes to qmtool (I hope!). We should have an updated alpha build in the next day or so and will email you when it's ready.
>
> Regards,
> Christopher Mayne
>
> PS. btw, in the files you sent me, the parameter file was the standard CGenFF parameter file, NOT the initialized file specific to your molecule. ffTK's reader for the "in-progress" parameter file doesn't handle the various odds and ends that the raw CGenFF file comes with, so make sure that you're generating the in-progress file using BuildPar.
>
>
>
> On Oct 23, 2013, at 12:38 PM, Mayne, Christopher G wrote:
>
>> This sounds like Gaussian has changed certain keywords in the log output with the G09 Rev D. We recently corrected some issues in this code a couple of days ago that might address this. Can you zip and send me the following files so that I can check?
>>
>> PSF file
>> PDB file
>> initial parameter file
>> hessian log file
>>
>> Regards,
>> Christopher Mayne
>>
>>
>> On Oct 23, 2013, at 10:03 AM, Shane O Mahony wrote:
>>
>>> Yes I am, I downloaded the most recent version of the alpha yesterday
>>> (23/10/13). But I get this problem with the currently released version
>>> as well.
>>>
>>> On 23 October 2013 15:49, John Stone <johns_at_ks.uiuc.edu> wrote:
>>>> Hi,
>>>> You'll need to tell us which precise VMD version you were running since
>>>> that directly relates to the version of the ffTK plugin that you
>>>> were therefore using. You mention that you're using the alpha version,
>>>> but it's best to be specific. Are you using the 1.9.2a33 version?
>>>>
>>>> Cheers,
>>>> John Stone
>>>> vmd_at_ks.uiuc.edu
>>>>
>>>>
>>>>
>>>> On Wed, Oct 23, 2013 at 03:29:46PM +0100, Shane O Mahony wrote:
>>>>> Hi,
>>>>>
>>>>> I'm having problems using the "optimise bonded" section of FFKT. I'm
>>>>> using the alpha version (this also occurs in the current release).
>>>>> When I click "Guess" in the "Parameters to optimize" subsection after
>>>>> inputted the needed files, I get the following error:
>>>>>
>>>>> can't use empty string as operand of "*"
>>>>> can't use empty string as operand of "*"
>>>>> while executing
>>>>> "expr {3*$natoms}"
>>>>> (procedure "::QMtool::load_gaussian_log" line 50)
>>>>> invoked from within
>>>>> "::QMtool::load_gaussian_log $hessLog $hessLogID"
>>>>> (procedure "::ForceFieldToolKit::gui::baoptGuessPars" line 46)
>>>>> invoked from within
>>>>> "::ForceFieldToolKit::gui::baoptGuessPars "
>>>>> invoked from within
>>>>> ".fftk_gui.hlf.nb.bondangleopt.pconstr.fftkGuessPars invoke "
>>>>> invoked from within
>>>>> ".fftk_gui.hlf.nb.bondangleopt.pconstr.fftkGuessPars instate {pressed
>>>>> !disabled} { .fftk_gui.hlf.nb.bondangleopt.pconstr.fftkGuessPars state
>>>>> !pressed; ..."
>>>>> (command bound to event)
>>>>>
>>>>> Any help would be appreciated,
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Shane
>>>>
>>>> --
>>>> 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/
>>
>>
>