Yes, I did it. But it does not look like a PBC problem because it did not fully disassociate.
Thank you
Nubia P. Toman
PhD student, Bioinformatics
Universidade Federal de Minas Gerais
________________________________
De: ABEL Stephane <Stephane.ABEL.cea.fr>
Enviado: quinta-feira, 16 de abril de 2020 10:31
Para: AMBER Mailing List <amber.ambermd.org>
Assunto: Re: [AMBER] protein-protein complex dissociation
Hi
If the complex returns to its initial state after some utime. Are you verify if it is not caused by the PBC ?
Stefane
________________________________________
De : Núbia Toman [nnubiaits.hotmail.com]
Envoyé : jeudi 16 avril 2020 15:17
À : amber.ambermd.org
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?
Best,
Nubia P. Toman
PhD student, Bioinformatics
Universidade Federal de Minas Gerais
