[AMBER] How to set up a simulation keeping crystal waters in the binding site

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Wed, 22 Sep 2021 20:00:12 +0500

Dear Amber users
I intend to simulate a protein-ligand complex; for which water molecules
seem to play an important role. I want to keep a few of the crystal waters
in the complex. How should I build the system topology and which force
field should I use? I have tried without water but my ligand starts moving
away from the binding site during simulation.
Any suggestions would be appreciated.
Thanks in advance.
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Received on Wed Sep 22 2021 - 08:30:02 PDT
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