[AMBER] Displacement of coordinated Zn during the simulation

From: Amit Sharma (Asstt. Prof., MCARS) <"Amit>
Date: Wed, 21 Jul 2021 20:57:08 +0530

Hi,

Cysteine coordinated Zn ion have got displaced from it's positions during
the MD run when the protein was subjected to certain external perturbation.

I wonder, if through the MD simulation can we also expect to see that the
displaced Zn ion will move back to it's normal coordination position, once
we remove the external perturbation?

Any suggestions (or references of MD simulation work using Amber) may be
helpful in which the movement of the coordinated ions (influenced by the
application or removal of any external perturbation on the protein system)
in or out of their coordination geometry has been observed previously.

Thank You,

Amit

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Received on Wed Jul 21 2021 - 08:30:02 PDT