VMD-L Mailing List

From: Chenbo Yan (ychenbo_at_umich.edu)
Date: Sat Aug 20 2022 - 07:43:52 CDT

Hi Andrew,

I have added the necessary files into the parameter folder. Thank you for
your time!
https://urldefense.com/v3/__https://drive.google.com/drive/folders/1ef60F5Rq3zWOrxmATPfo-CFeqAUN4_IE?usp=sharing__;!!DZ3fjg!8hpNnZ7CW0Q6W0DJVdGH2ZsIShmghJtJMa5MkosG0AfWayMAbzp0Gea4PqnZO3RsyZOCSCs6JHBGNM7D-E1d$

Best regards,
Chenbo

On Fri, Aug 19, 2022 at 9:40 AM Pang, Yui Tik <andrewpang_at_gatech.edu> wrote:

> Hi Chenbo,
>
> Would you mind sharing your psf and pdb files as well, so that we can try
> to reproduce the issue?
>
> Andrew
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Chenbo Yan <ychenbo_at_umich.edu>
> *Sent:* Thursday, August 18, 2022 10:31 PM
> *To:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* vmd-l: Error in FFTK charges optimization (Run Optimization)
>
> Hello,
>
> I am trying to parameterize the *Alexa* Fluor *594* dye following the
> FFTK tutorial with ORCA. I am stuck at the Run Optimization step in the
> charges optimization section due to the following error:
>
> atomselect set: 0 data items doesn't match 1 selected atoms.
> atomselect set: 0 data items doesn't match 1 selected atoms.
> while executing
> "$temp set x [lindex [lindex $molCoords $i] 0]"
> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 194)
> invoked from within
> "::ForceFieldToolKit::ChargeOpt::optimize"
> (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
> invoked from within
> "::ForceFieldToolKit::gui::coptRunOpt "
> invoked from within
> ".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
> invoked from within
> ".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} {
> .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed;
> .fftk_gui.hlf.nb.chargeopt.runOpt in..."
> (command bound to event)
>
> I have read in a previous thread that this error could be caused by
> non-converge water interaction calculations, so I have made sure all the
> ORCA output files result in convergence, but the error still persists.
>
> The output files are in the link below, any help would be greatly
> appreciated!
>
> https://urldefense.com/v3/__https://drive.google.com/drive/folders/1ef60F5Rq3zWOrxmATPfo-CFeqAUN4_IE?usp=sharing__;!!DZ3fjg!8hpNnZ7CW0Q6W0DJVdGH2ZsIShmghJtJMa5MkosG0AfWayMAbzp0Gea4PqnZO3RsyZOCSCs6JHBGNM7D-E1d$
> <https://urldefense.com/v3/__https://drive.google.com/drive/folders/1ef60F5Rq3zWOrxmATPfo-CFeqAUN4_IE?usp=sharing__;!!DZ3fjg!5ECwuLG7hC85dYJl4cEzLAjjQCZhxtP1ZjCSsslwp667vepn6ggIBmwsm1pzLVpwoPqqH19hx82IueXQ8slu$>
>
> Thanks!
> Chenbo
>
>