VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Fri Nov 03 2017 - 10:39:20 CDT

I’m glad you found a solution. I just confirmed it works on linux and mac both for me. Sorry that it took so long to sort out.

I’m committing the change to the VMD CVS so that it will appear in future versions.

Best,
JC

> On Nov 2, 2017, at 10:27 AM, Matt Albertolle <matt.albertolle_at_gmail.com> wrote:
>
> Hey JC,
>
> Thanks for the patch! We still could not get this to work with the Linux build of VMD (1.9.3 and 1.9.4), but we tried it on the Windows build (1.9.3) and it worked fine!! Thanks again for the support.
>
> Matt
>
> On Tue, Oct 24, 2017 at 6:08 PM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
> Wow, I think you found a new gaussian revision (g09_revD.01) that breaks the parser! This is strange because I thought we would have caught this by now. I finally tracked it down to the fact that this version uses the line “Z-Matrix found in file.”, which is not in any gaussian log we’ve seen before. I’m still shocked that they keep changing minor things like this between revisions.
>
> Try replacing the corresponding file in your …/VMD 1.9.4/Contents/vmd/plugins/noarch/tcl/qmtool1.3/ directory with the attached one (I’m not sure what OS you’re using so the precise directory location will vary). Let me know if it works.
>
> Best,
> JC
>
>
>> On Oct 23, 2017, at 7:40 PM, Matt Albertolle <matt.albertolle_at_gmail.com <mailto:matt.albertolle_at_gmail.com>> wrote:
>>
>> Hi,
>>
>> Please find the following compressed files:
>>
>> bond_ang_opt_err.log (Error From fftk)
>> CH3-SOH_opt.pdb (Original PDB)
>> ch3oh.1.psf (Original PSF)
>> ch3oh.hess.chk.log (Gaussian09 Output)
>> ch3oh.hess.gau (Gaussian input)
>> CH3SOH.0.par (In-Progress parameter file)
>>
>> We received this error in step 5.2 of the fftk tutorial (http://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf <http://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf>) when using the Guess button to populate the Parameters to Optimize.
>>
>> We are not necessarily sure if this error arose from the way we calculated in Gaussian or from a potential problem with fftk not being able to recognize the gaussian log file correctly.
>>
>> Thanks and if you need any other files please let me know.
>>
>> Matt
>>
>> On Fri, Oct 20, 2017 at 5:15 PM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
>> Hi Matt,
>>
>> I first need all the input files necessary to reproduce the error.
>>
>> Best,
>> JC
>>
>>> On Oct 12, 2017, at 12:30 PM, Matt Albertolle <matt.albertolle_at_gmail.com <mailto:matt.albertolle_at_gmail.com>> wrote:
>>>
>>> Hello
>>>
>>> We are currently experiencing issues inputting the gaussian output .log file into the VMD fftk. We have looked into older posts to this mailing list and saw that others have had a similar problem with VMD not being able to parse the coordinate data efficiently. I have included the VMD output error and our output file from Gaussian. Please let me know if you need any other input files.
>>>
>>> Software Versions Used
>>>
>>> Gaussian09 (g09_revD.01-x86_64)
>>>
>>> VMD 1.9.3
>>>
>>> Thanks in advance for your help.
>>>
>>> Matt
>>>
>>> <VMDfftkErrorFiles.zip>
>>
>>
>> <fftk_error.tar.gz>
>
>
>