How to preparation ligand database in MOE?

03 August 2023 1 6K Report

Hello, everyone.

I am trying to do docking in MOE. I tried protonating 100 ligands in the same order, but the system said that the size of the vector was exceeded. Do you know how I can correct this? Or what is the maximum size of the matrix to protonate?

or what is the correct procedure to prepare the ligands in MOE? :(

Ricardo J Ferreira

Hi,

the best way is to do it already in the database. Create a database with all you ligands and then Compute -> Molecule -> Wash. Here you define protonation states and all the rest.

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