Hi Sargis,
I am trying to prepare ligands from .sdf file downloaded (Natural Products Set II: https://wiki.nci.nih.gov/display/NCIDTP ... pound+Sets) for the virtual screening using PyRx 0.9 on OSX 10.11.1
After adding the .sdf file as input using 'control' tab 'OpenBabel', I do energy minimization to all ligands and then I convert all the ligands into pdbqt formate. But, unfortunately I keep getting this (attached file) error and I am not able to figure out how to fix this problem. Could you please guide me to fix this problem. I wonder if there is a standard way of pre-processing the .sdf file with multiple ligands which one should go through before any enery minimization and pdbqt conversion.
Note: It's not the only .sdf file that gives me such error, there are other files too. Please see the attached error log file.
Thanks,
Ajeet
NIH/NIDCR