GromacsError: Structure contains PROA molecules, but no template defined Exiting.
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imren bayıl
May 26, 2023, 1:40:37 PM5/26/23
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I have used this command
gmx trjconv -s step5.tpr -f md_noPBC.xtc -fit rot+trans -o md_fit.xtc -n index.ndx
gmx trjconv -s step5.tpr -f md_noPBC.xtc -fit rot+trans -o md_fit.xtc -n index.ndx
Then
gmx_MMPBSA -O -i mmpbsa.in -cs step5.tpr -ci index.ndx -cg 1 13 -ct md_fit.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA1.dat -eo FINAL_RESULTS_MMPBSA1.csv
GromacsError: Structure contains PROA molecules, but no template defined
Exiting. All files have been retained.
Exiting. All files have been retained.
Mario Sergio Valdes
May 26, 2023, 1:42:56 PM5/26/23
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Please, attach the top file
imren bayıl
May 26, 2023, 2:03:30 PM5/26/23
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26 Mayıs 2023 Cuma tarihinde saat 20:42:56 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:
Mario Sergio Valdes
May 26, 2023, 2:08:33 PM5/26/23
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Is the toppar folder in the same directory as the top file?
imren bayıl
May 26, 2023, 2:11:23 PM5/26/23
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imren bayıl
May 26, 2023, 2:26:26 PM5/26/23
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so Could you tell me where is my fault
26 Mayıs 2023 Cuma tarihinde saat 21:11:23 UTC+3 itibarıyla imren bayıl şunları yazdı:
Mario Sergio Valdes
May 26, 2023, 2:29:04 PM5/26/23
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Please, send me the top and the toppar folder to check what's going on
imren bayıl
May 26, 2023, 2:34:46 PM5/26/23
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imren bayıl
May 26, 2023, 2:36:07 PM5/26/23
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26 Mayıs 2023 Cuma tarihinde saat 21:35:25 UTC+3 itibarıyla imren bayıl şunları yazdı:
imren bayıl
May 26, 2023, 2:36:41 PM5/26/23
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26 Mayıs 2023 Cuma tarihinde saat 21:36:07 UTC+3 itibarıyla imren bayıl şunları yazdı:
Mario Sergio Valdes
May 26, 2023, 2:46:38 PM5/26/23
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please, compress all in a file and attach it
imren bayıl
May 26, 2023, 2:54:35 PM5/26/23
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also I got same error different molecules
GromacsError: Structure contains UNK molecules, but no template defined
Exiting. All files have been retained.
26 Mayıs 2023 Cuma tarihinde saat 21:46:38 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:
Mario Sergio Valdes
May 26, 2023, 2:58:07 PM5/26/23
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I can't reproduce the problem if you don't send me the files... please, compress the top and folder toppar in a file and attach it
Mario Sergio Valdes
May 26, 2023, 3:10:31 PM5/26/23
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Please, follow these instructions:
- create a new folder called files (right click --> New Folder)
- Select the topol.top and folder toppar (Hold the Ctrl key and click them)
- Copy (Press Ctrl + C or right click --> copy)
- Double-click in the "files" folder to open it
- Paste (Press Ctrl + V or right click --> paste)
- Get back to the parent folder
- Right-click in the "files" folder --> Compress --> Create
- Attach the "files.zip" file to a new mail here
imren bayıl
May 26, 2023, 3:34:20 PM5/26/23
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26 Mayıs 2023 Cuma tarihinde saat 22:10:31 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:
imren bayıl
May 26, 2023, 3:39:11 PM5/26/23
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https://drive.google.com/drive/u/1/folders/1joCmIllg54SQ0yKMswxdHSAtOu9e6BYx
26 Mayıs 2023 Cuma tarihinde saat 22:34:20 UTC+3 itibarıyla imren bayıl şunları yazdı:
Mario Sergio Valdes
May 26, 2023, 3:41:09 PM5/26/23
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Please, note that the forcefield.itp, TIP3P.itp, and UNK.itp are empty... That's the problem
imren bayıl
May 26, 2023, 4:54:26 PM5/26/23
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many thanks
26 Mayıs 2023 Cuma tarihinde saat 22:41:09 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:
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