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Article ID: 91 - Last Modified: May 4, 2011

I'd like to perform a mutation via FEP, but the fragment I want is not listed in the fragment library. Can I still perform the mutation?

In most cases, yes. Follow the directions in the mutation FEP panel as usual, but select a fragment that is similar to the fragment you ultimately want. Use the 'View' button to display the fragment, and edit the fragment using Maestro's build tools. Make sure to change atom types, delete atoms, change bond orders, and so on. In Suite 2009 you may not add any atoms, so you will have to choose a fragment that has enough atoms with the right connectivity. From Suite 2010 on, this restriction no longer exists. However, the quality of the results goes down as the mutation gets larger, so you should restrict the size of the mutation for best results.

Keywords: Desmond, Maestro

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