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This formed a multi-conformer sdf "L-Prolylglycine__input2881.sdf" (within the zipped file). Converted it to pdbqt with obabel. I used two flags: -m and -writeconformers obabel -isdf input.sdf -O drug.pdbqt --writeconformers -m
It wrote a really large 3D PDBQT. Making directly in obabel from SMILE gives a normal molecule.
This is the same for several molecules
Please suggest changes to the process to avoid this issue L-proglycine.zip
Thank you,
Regards
EDIT: On ubuntu 24.04 and the latest version of Gypsum_DL
The text was updated successfully, but these errors were encountered:
OC(=O)CNC(=O)C1CCCN1 L-Prolylglycine
This formed a multi-conformer sdf "L-Prolylglycine__input2881.sdf" (within the zipped file). Converted it to pdbqt with obabel. I used two flags: -m and -writeconformers
obabel -isdf input.sdf -O drug.pdbqt --writeconformers -m
It wrote a really large 3D PDBQT. Making directly in obabel from SMILE gives a normal molecule.
This is the same for several molecules
Please suggest changes to the process to avoid this issue
L-proglycine.zip
Thank you,
Regards
EDIT: On ubuntu 24.04 and the latest version of Gypsum_DL
The text was updated successfully, but these errors were encountered: