ADL: Generating mol2 ligand files

josh at josh at
Wed Aug 5 04:40:35 PDT 2020

   Hey guys, hope everybody is well.

   I have a quick question about generating ligand files. Occasionally when I
   use AutodockTools’ PDBQT conversion tool, it does not recognise some atomic
   charges correctly which leads to inaccurate docking.

   Instead I have been using the AM1-BCC forcefield in Chimera software to
   generate mol2 files, and this works much better. In my research group this
   works  fine,  but  we  have some commercial collaborators who are also
   interested in docking, and are looking to avoid license fees! Does anybody
   know of alternative atomic charge generation software that is free for
   commercial use? I know AmberTools20 might be a good idea, but wondered if
   there are any other programs I may be missing!

   Thank you guys!

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