[AMBER] Creating library files - optimised or docked structure?

From: Sam Walsworth (Researcher) <"Sam>
Date: Wed, 22 Dec 2021 00:45:09 +0000


When you create library files with leap, is it best to do this using an optimised structure (I have parameters for silver-containing bonds and angles, as well as RESP charges for the optimised structures) or using a docked structure which better represents the ligands conformation at the start of an MD simulation? I imagine it'd be the optimised structure, and this is then used when you create the enzyme-ligand complex in leap.

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Received on Tue Dec 21 2021 - 17:00:02 PST
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