In preparation for a virtual screening, PyRx was used to convert the molecules from sdf format to pdbqt, but noticed a lot of the molecules came out as shown attached. I need help to know what was done wrongly?
Thank you Suresh Kumar. But how do I use OpenBabel to convert 5,000 molecules from SDF to PDB? (I know how to use it to convert individual molecules but not in bulk) It was when I couldn't use OpenBabel to do the conversion that I resolved to using PyRx to convert directly from SDF to PDBQT. Though, I minimized all the molecules before conversion and some still came out as shown in the picture above.
I guess I am not wrong. Select all the files you need to convert in the input file box. In the output file box, give the name as "*.pdb" ( without quotes). After you press convert, you will find all the files converted as needed.
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