Hello everyone, I have a problem while trying to generate pdbqt files and have them minimized. I keep getting this error (see bottom) when trying to generate big files. The mol2 contains 140000 molecules downloaded from Zinc and I just want to convert them in pdbqt and have them minimized to be able to dock them. Any suggestions?
Also, if I try to do the same thing but from an SDF file I get another error “could not set up force field” and the program just stops. * Run with command: “obabel 145485.mol2 -O 145485.pdbqt --minimize --MMFF94 --sd” ============================== *** Open Babel Warning in OpenBabel::MOL2Format::ReadMolecule Failed to kekulize aromatic bonds in MOL2 file (title is ZINC000002923609) ============================== *** Open Babel Warning in OpenBabel::MOL2Format::ReadMolecule Failed to kekulize aromatic bonds in MOL2 file (title is ZINC000001725928) Thanks
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