Issue with Gypsum

[Roco Riveros]

Hi! An error with Gypsum appeared. Can you help me to understand what happened?

GOT LIGANDS FROM THE LAST GENERATION
CONVERTING SMILES TO SDF
The Following ligands Failed to convert in Gypsum
Likely due to a Timeout
[‘Gen_1_Mutant_85_789005’, ‘Gen_1_Mutant_85_430308’, ‘Gen_1_Mutant_85_258862’, ‘Gen_1_Mutant_85_520726’, ‘Gen_1_Mutant_85_602865’, ‘Gen_1_Mutant_44_305980’, ‘Gen_1_Mutant_85_510212’, ‘Gen_1_Mutant_44_715734’, ‘Gen_1_Mutant_85_480584’, ‘Gen_1_Mutant_44_99444’, ‘Gen_1_Mutant_44_397804’, ‘Gen_1_Mutant_44_796769’, ‘Gen_1_Mutant_85_259219’, ‘Gen_1_Mutant_44_888145’, ‘Gen_1_Mutant_44_981696’, ‘Gen_1_Mutant_44_201290’, ‘Gen_1_Mutant_44_607594’, ‘Gen_1_Mutant_44_425103’, ‘Gen_1_Mutant_44_479517’, ‘Gen_1_Mutant_85_361019’, ‘Gen_1_Mutant_85_49762’, ‘Gen_1_Mutant_85_254178’, ‘Gen_1_Mutant_85_637281’, ‘Gen_1_Mutant_44_683721’, ‘Gen_1_Mutant_85_45266’, ‘Gen_1_Mutant_85_652445’, ‘Gen_1_Mutant_85_672883’, ‘Gen_1_Mutant_85_712413’, ‘Gen_1_Mutant_85_871923’, ‘Gen_1_Mutant_85_77916’, ‘Gen_1_Mutant_44_371590’, ‘Gen_1_Mutant_44_633122’, ‘Gen_1_Mutant_85_553580’, ‘Gen_1_Mutant_85_322509’, ‘Gen_1_Mutant_44_574058’, ‘Gen_1_Mutant_44_868727’, ‘Gen_1_Mutant_85_394033’, ‘Gen_1_Mutant_44_613922’, ‘Gen_1_Mutant_68_293882’, ‘Gen_1_Mutant_44_152856’, ‘Gen_1_Mutant_44_364432’, ‘Gen_1_Mutant_44_829565’, ‘Gen_1_Mutant_85_3702’, ‘Gen_1_Mutant_85_572257’, ‘Gen_1_Mutant_44_383296’, ‘Gen_1_Mutant_44_239244’, ‘Gen_1_Mutant_85_502092’, ‘Gen_1_Mutant_44_44625’, ‘Gen_1_Mutant_44_715203’, ‘Gen_1_Mutant_85_418098’]
CONVERTING SMILES TO SDF COMPLETED
CONVERTING SDF TO PDB

There are no sdf’s to convert to PDB’s. There may be an issue with Gypsum.

Can you help me to solve this issue?
Thank you!

[Jacob Durrant]

Hi Roco. Much thanks for your interest in AutoGrow4. I believe AutoGrow4 does generate SDF files internally, which it passes to Gypsum-DL for processing. What you’re seeing is more of a warning than an error. AutoGrow4 has created a few ligands that Gypsum-DL apparently can’t handle, so it’s moved on to other compounds.

Can you confirm that it did generate some compounds in the end? As long as it did manage to generate some output ligands, you can safely ignore these warnings.

Take care.

[Rocio Riveros]

I got it! Finally, it generated molecules at the end.

Thank you very much!

[Jacob Durrant]

Happy to hear you got it to work, Rocio! Take care.

[Author]

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