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ERROR: RDKit cannot read MOL2 structure None #5

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wowfee opened this issue Nov 21, 2020 · 1 comment
Open

ERROR: RDKit cannot read MOL2 structure None #5

wowfee opened this issue Nov 21, 2020 · 1 comment

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@wowfee
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wowfee commented Nov 21, 2020

hello, I use the mol2 file which could be used when I get the top file, but once I use at "my_ligand = Ligand("./",ligand_pdb,ligand_mol2)" command, it gives the error: RDKit cannot read MOL2 structure None, could you please give me any suggestions about this? thank you!

@DKokh
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DKokh commented Dec 15, 2020

RDkit is very sensitive to the format of mol2 file. To fix the mol2 file one can try to use http://www.swissparam.ch/

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