pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
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Incorrect conversion of some ligands #64

Closed nyubachi closed 1 year ago

nyubachi commented 1 year ago

Thank you for providing us with a great product.

I am using "Protein_ligand.ipynb", but I am having problems with some ligands. For example, I have Stearic Acid (CCCCCCCCCCCCCCCCCCCCCCCC(=O)O) as a ligand, set "Add_ligand_hydrogens: Yes" and when I run to the "Enumerate Stereoisomers to generate ligand topology:" cell, it is converted to the ligand as shown in the attached image.

Is there any way to resolve this issue?

inappropriate_ligand
nyubachi commented 1 year ago

I am closing this issue because I think there is something wrong with my ligand file or it is a glitch in the current version of Openbabel.