[AMBER] problem in the protein-ligand system

From: Renato Araujo <renatoacufpa.gmail.com>
Date: Thu, 10 Feb 2022 10:52:19 -0300

Dear amber users

I'm facing a problem in a protein-binding simulation

I'm trying to simulate 100ns of molecular dynamics.

I made the coupling and later the Dynamic process

1) In the initial 40ns, my ligand moves away from the binding site and
consequently from the enzyme.

What can I do to solve this problem?

2) When preparing the system in tleap, I notice that a Na+ is placed very
close to my ligand and remains there during the entire simulation time, is
this a problem? if yes how to solve?

follow the image

thanks

-- 
Prof Dr Renato Costa
Instituto Federal do Pará - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55  91 985484622

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Received on Thu Feb 10 2022 - 06:00:02 PST