Search found 2 matches
Search found 2 matches • Page 1 of 1
- Thu Mar 24, 2022 1:32 am
- Forum: Main Forum
- Topic: converting .sdf files to .pdb/.pdbqt
- Replies: 1
- Views: 418
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...
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 ...