converting .sdf files to .pdb/.pdbqt

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Moderator: robpearc

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converting .sdf files to .pdb/.pdbqt

Post by koesuki123 »

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 solutions or alternatives to convert the ligands simultaneoImage[/img]usly without changing the structure?
Screenshot (219).png (142.36 KiB) Viewed 437 times
Posts: 36
Joined: Wed Nov 03, 2021 5:59 pm

Re: converting .sdf files to .pdb/.pdbqt

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We are not maintainer or developer of OpenBabel and are not entitled to assist you with the issue. You should ask your questions at
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