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Tinker: Software Tools for Molecular Design
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Poledit issue with Phosphric acid #77

Closed misterbrandonwalker closed 3 years ago

misterbrandonwalker commented 3 years ago

Hi Dr. Ponder, We seem to have found an issue with current poledit.x file. There is a poor RMSPD shown in KeyOut.txt (at the bottom). The issue was compounded when we averaged the multipoles. Tinker 8.7 seems to provide reasonable results.

AveragedKeyOut.txt Phosphoricacid.pot.txt Phosphoricacid_oldpoledit.txt CorrectOutput.txt Phosphoricacid.key.txt Phosphoricacid.key_2.txt KeyOut.txt Phosphoricacid.xyz_2.txt

Commands and output are in KeyOut.txt and AveratedKeyOut.txt , the correct output is in CorrectOutput.txt using older tinker version (like 8.7 something).

Thanks for your time!

pren commented 3 years ago

This is not due to POLEDIT. The issue is with our own average script.

From: Brandon Walker notifications@github.com Sent: Thursday, December 17, 2020 12:48 PM To: TinkerTools/tinker tinker@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [TinkerTools/tinker] Poledit issue with Phosphric acid (#77)

Hi Dr. Ponder, We seem to have found an issue with current poledit.x file. There is a poor RMSPD shown in KeyOut.txt (at the bottom). The issue was compounded when we averaged the multipoles. Tinker 8.7 seems to provide reasonable results.

AveragedKeyOut.txthttps://github.com/TinkerTools/tinker/files/5711506/AveragedKeyOut.txt Phosphoricacid.pot.txthttps://github.com/TinkerTools/tinker/files/5711507/Phosphoricacid.pot.txt Phosphoricacid_oldpoledit.txthttps://github.com/TinkerTools/tinker/files/5711508/Phosphoricacid_oldpoledit.txt CorrectOutput.txthttps://github.com/TinkerTools/tinker/files/5711509/CorrectOutput.txt Phosphoricacid.key.txthttps://github.com/TinkerTools/tinker/files/5711510/Phosphoricacid.key.txt Phosphoricacid.key_2.txthttps://github.com/TinkerTools/tinker/files/5711511/Phosphoricacid.key_2.txt KeyOut.txthttps://github.com/TinkerTools/tinker/files/5711512/KeyOut.txt Phosphoricacid.xyz_2.txthttps://github.com/TinkerTools/tinker/files/5711513/Phosphoricacid.xyz_2.txt

Commands and output are in KeyOut.txt and AveratedKeyOut.txt , the correct output is in CorrectOutput.txt using older tinker version (like 8.7 something).

Thanks for your time!

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misterbrandonwalker commented 3 years ago

Correction, I was comparing 8.8 (which i called correct but that label may not be appropriate) and 8.8.7. The latest poledit has frames on atom P repeated twice ( I guess not huge deal).

On Thu, Dec 17, 2020 at 1:19 PM Pengyu Ren notifications@github.com wrote:

This is not due to POLEDIT. The issue is with our own average script.

From: Brandon Walker notifications@github.com Sent: Thursday, December 17, 2020 12:48 PM To: TinkerTools/tinker tinker@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [TinkerTools/tinker] Poledit issue with Phosphric acid (#77)

Hi Dr. Ponder, We seem to have found an issue with current poledit.x file. There is a poor RMSPD shown in KeyOut.txt (at the bottom). The issue was compounded when we averaged the multipoles. Tinker 8.7 seems to provide reasonable results.

AveragedKeyOut.txt< https://github.com/TinkerTools/tinker/files/5711506/AveragedKeyOut.txt> Phosphoricacid.pot.txt< https://github.com/TinkerTools/tinker/files/5711507/Phosphoricacid.pot.txt>

Phosphoricacid_oldpoledit.txt< https://github.com/TinkerTools/tinker/files/5711508/Phosphoricacid_oldpoledit.txt>

CorrectOutput.txt< https://github.com/TinkerTools/tinker/files/5711509/CorrectOutput.txt> Phosphoricacid.key.txt< https://github.com/TinkerTools/tinker/files/5711510/Phosphoricacid.key.txt>

Phosphoricacid.key_2.txt< https://github.com/TinkerTools/tinker/files/5711511/Phosphoricacid.key_2.txt>

KeyOut.txthttps://github.com/TinkerTools/tinker/files/5711512/KeyOut.txt

Phosphoricacid.xyz_2.txt< https://github.com/TinkerTools/tinker/files/5711513/Phosphoricacid.xyz_2.txt>

Commands and output are in KeyOut.txt and AveratedKeyOut.txt , the correct output is in CorrectOutput.txt using older tinker version (like 8.7 something).

Thanks for your time!

  • Brandon

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misterbrandonwalker commented 3 years ago

Actually we found bug in how poltype parses and it was not expecting empty spaces on frame definition (it undersands 0 to mean empty atom in frame definition).