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

From: Carlos Simmerling <>
Date: Wed, 22 Sep 2021 11:30:28 -0400

if you include the crystal water molecules in the pdb file when you run
leap, they should be included in the simulation. are you finding any errors
doing this?

On Wed, Sep 22, 2021 at 11:00 AM Sadaf Rani <> wrote:

> 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.
> Sadaf
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Received on Wed Sep 22 2021 - 09:00:02 PDT
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