VMD-L Mailing List

From: Pang, Yui Tik (andrewpang_at_gatech.edu)
Date: Sun Aug 28 2022 - 20:03:48 CDT

Hi Chenbo,

Sorry for the late reply. Appoint further inspection, unfortunately, I think none of your calculations are completed. You should see “****ORCA TERMINATED NORMALLY****” at the end of the output files if the calculation is completed correctly, as in the one you had for parameters/wat-sp.out. Your molecule is quite large for QM calculations. I would suggest you to break it down into smaller pieces and run the calculation for each part individually (See https://urldefense.com/v3/__http://www.ncbi.nlm.nih.gov/pubmed/26280362__;!!DZ3fjg!4AGE7PIsWHpyDzN_rlIu0yeB8hcLkyXm-GVkgMcXlgamwQjv8QZgplW_o1JLEUNuvN-r3TxW6JFBvQff1WRNbL7W$ ). You also need to check the output structures carefully using “Load QM Output Files” button under the “Water Int.” tab to make sure none of them have water clashing, e.g. AF594-ACC-O3-120b (See above paper). Lastly, ffTK was originally written to support ORCA4. Using a different version may run into output format issues. I would suggest you to rerun your calculations using ORCA4 if possible.

Hope the above information helps.

Best,
Andrew

From: Chenbo Yan<mailto:ychenbo_at_umich.edu>
Sent: Saturday, August 20, 2022 8:44 AM
To: Pang, Yui Tik<mailto:andrewpang_at_gatech.edu>
Cc: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Error in FFTK charges optimization (Run Optimization)

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!4AGE7PIsWHpyDzN_rlIu0yeB8hcLkyXm-GVkgMcXlgamwQjv8QZgplW_o1JLEUNuvN-r3TxW6JFBvQff1aJMDOYP$

Best regards,
Chenbo

On Fri, Aug 19, 2022 at 9:40 AM Pang, Yui Tik <andrewpang_at_gatech.edu<mailto: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<mailto:owner-vmd-l_at_ks.uiuc.edu> <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of Chenbo Yan <ychenbo_at_umich.edu<mailto:ychenbo_at_umich.edu>>
Sent: Thursday, August 18, 2022 10:31 PM
To: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu<mailto: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!4AGE7PIsWHpyDzN_rlIu0yeB8hcLkyXm-GVkgMcXlgamwQjv8QZgplW_o1JLEUNuvN-r3TxW6JFBvQff1aJMDOYP$ <https://urldefense.com/v3/__https:/drive.google.com/drive/folders/1ef60F5Rq3zWOrxmATPfo-CFeqAUN4_IE?usp=sharing__;!!DZ3fjg!5ECwuLG7hC85dYJl4cEzLAjjQCZhxtP1ZjCSsslwp667vepn6ggIBmwsm1pzLVpwoPqqH19hx82IueXQ8slu$>

Thanks!
Chenbo


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