Search found 2 matches

by koesuki123
Thu Mar 24, 2022 1:32 am
Forum: Main Forum
Topic: converting .sdf files to .pdb/.pdbqt
Replies: 1
Views: 418

converting .sdf files to .pdb/.pdbqt

Hi. I want to convert ~4000 ligands in .sdf files into .pdb or .pdbqt format for molecular docking. I used " >obabel *.sdf -opdb -m " command but the structure of the ligands deformed. attached is the picture of one of the ligand after conversion to pdb. is there any reason for this? any s...
by koesuki123
Tue Dec 14, 2021 12:06 pm
Forum: Main Forum
Topic: issues with docking result
Replies: 1
Views: 613

issues with docking result

Hello. I accidentally prepared and docked two files of same ligand. I use Avogadro to optimize both of these ligands files. However, the docking result (on same protein) indicated that both of these ligands had different binding energies and poses. So I want to ask if it is normal to have different ...