failure to convert sdf files to pdbqt

[Shakeel1679]

while preparing ligands for vs the program failed to convert a file of 300 ligands in sdf form to pdbqt

[DUTchecheche]

A molecule file in sdf format uses the flag "$$$$" as a marker for the end of a single molecule. Possible reasons for your failure:

1. Some unexpected errors prevented the use of "$$$$" to split the whole sdf file. (Check whether the "split_database" folder was successfully generated? Are there split single molecule files in the folder? It can be found in the saving directory.)
2. Unknown errors in the single molecule file prevents OpenBabel from converting the molecular format correctly, such as molecules containing metal elements, ionic compounds, and so on.

A demo of a molecule file containing 3 ligands in sdf format has been added to the attachment. (remember to change it to sdf format) ligands.txt