VMD-L Mailing List

From: Alexandre Suman de Araújo (alexandre.suman_at_unesp.br)
Date: Wed Nov 18 2020 - 15:44:56 CST

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
>
>