Hello Everyone, I am converting a PDBQT file from Vina docked conformations to SDF with Openbabel.
The problem is the hydrogens are not added correctly during PDBQT to SDF conversion. I found a suggestion here: https://sourceforge.net/p/openbabel/mailman/message/37237701/. Is a similar command line approach possible in openbabel , where reference 3D structure (with correct bond orders) and docked PDBQT coordinates could lead to valid SDF files? If not, is there an alternative solution? Best Regards, Mandar Kulkarni
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