Can I run a Desmond FEP job with a fragment that isn't in the list in the Ligand functional group mutation panel?

If the fragment you want to use for ligand functional group mutation isn't in the list, you can edit an existing fragment to obtain the desired fragment, using the Workspace editing tools.

In Suite 2008, you cannot add atoms to the fragment, so the fragment you modify must contain all the atoms that are needed. You can change the element and bond orders and delete atoms to create the desired fragment.

Keywords: Desmond, fragment, ligand functional group

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