VMD-L Mailing List

From: Mariano Spivak (mariano_at_ks.uiuc.edu)
Date: Mon Nov 23 2020 - 17:24:53 CST

Hi Alexandre and Andrew,

Sorry for the late reply. I fixed the issue with the latest qmtool version. The fix will be present in the next alpha release of VMD.
For the meantime, you can replace the linked file into the qmtool directory. The directory is usually located in your VMD installation directory under plugins/noarch/tcl/qmtool

https://uofi.box.com/s/93ngf0vfe7crw4p0pnaln49o4u2m7921
 <https://uofi.box.com/s/93ngf0vfe7crw4p0pnaln49o4u2m7921>
If you have any questions regarding this, please let me know.

Best

> On Nov 18, 2020, at 3:44 PM, Alexandre Suman de Araújo <alexandre.suman_at_unesp.br> wrote:
>
> Hi Andrew.
>
> Thank you for your response.
>
> I will try to use the log files in the charge optimization.
>
> Hope you can fix this ASAP.
>
> Regards
> --
> Prof. Dr. Alexandre Suman de Araujo
> Departamento de Física
> Instituto de Biociências, Letras e Ciências Exatas - IBILCE
> Universidade Estadual Paulista
> e-mail:
> asaraujo_at_ibilce.unesp.br
>
> Phone: +55 (17) 3221-2566/3221-2240
>
>
>
> Em qua., 18 de nov. de 2020 às 18:15, Pang, Yui Tik <andrewpang_at_gatech.edu> escreveu:
> Hi Alexandre,
>
> ffTK relies on QMTools to read the Gaussian log files. Unfortunately, there is a bug in the latest version of QMTools that it did not read the minimization trajectory correctly, ending with the error you seen. We are communicating with Dr. Spivak (cced here) to fix the issue. As far as I know, the bug does not affect the charge optimization process. At the meantime, you may use an older version of VMD (e.g. 1.9.3) to read the log file, but I still recommend using the ffTK from the latest version of VMD to perform parameter optimization.
>
> Thank you.
>
> Andrew
> Graduate student in JC Gumbart's Lab
> From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Alexandre Suman de Araújo <alexandre.suman_at_unesp.br>
> Sent: Monday, November 16, 2020 9:49 AM
> To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> Subject: vmd-l: Error "vecscale: parameters must have data" in water interaction step of FFTK
>
> Hi all.
>
> I used the paramchem site to obtain a first model for a ligand, and I am refining the high penalized parameters with FFTK.
>
> So I optimized the molecule geometry, and everything was ok.
>
> In the water interaction step, I loaded the psf and the optimized pdb, defined the atoms I want to refine the partial charge that could form hydrogen bonds with water (donors and acceptors), and wrote the input QM files. When I try to load these input files to observe the position of the water molecules, I have the error cited in the email subject.
>
> The .log file, along with .psf and .pdb ligand files, is attached.
>
> Could anyone help me with this issue?
>
> Regards
> --
> Prof. Dr. Alexandre Suman de Araujo
> Departamento de Física
> Instituto de Biociências, Letras e Ciências Exatas - IBILCE
> Universidade Estadual Paulista
> e-mail:
> asaraujo_at_ibilce.unesp.br
>
> Phone: +55 (17) 3221-2566/3221-2240
>