Re: [AMBER] protein-protein complex dissociation

From: ABEL Stephane <>
Date: Thu, 16 Apr 2020 13:31:34 +0000


If the complex returns to its initial state after some utime. Are you verify if it is not caused by the PBC ?

De : Núbia Toman []
Envoyé : jeudi 16 avril 2020 15:17
À :
Objet : [AMBER] protein-protein complex dissociation

Dear Amber users,

I performed 1 us MD simulation of a protein-protein complex. After about 200ns the complex seemed to start to disassociate and continued partially dissociated 70% of the simulation after that it returns to its initial position (bound).

This system has a mutation that drastically decreases the binding affinity and the simulation results seemed to agree with experimental data. But I am wondering if this partial dissociation is a random thing or could be due to the effect of the mutation.

Can anyone help me with that?


Nubia P. Toman
PhD student, Bioinformatics
Universidade Federal de Minas Gerais

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Received on Thu Apr 16 2020 - 07:00:02 PDT
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