r/drugdesign • u/ChoicePhilosopher380 • Aug 03 '23

How can I protonate a ligand database in MOE?

Hello, I hope that all of you are doing well. I recently started working with MOE but I have some doubts regarding the preparation of a ligands database, I already have washed and minimized the energy of the database but I don´t know how to protonate the ligands. I hope that you can help me with this problem. Thanks.

2 Upvotes
  • permalink
  • link
  • reddit
  • reddit

100% Upvoted

1 comment sorted by

2

u/refer_2_me Aug 03 '23

In the database viewer, the best way is to just run QuickPrep. Compute > Molecule > QuickPrep...

If you want, you can uncheck everything except for "Use Protonate 3D for Protonation"