Is the change continuous with no jumps in the profiles like distances?
On Thu, Apr 16, 2020, 9:36 AM Núbia Toman <nnubiaits.hotmail.com> wrote:
> Yes, I have done it.
> Also tried several combinations of the autoimage to verify it was a
> re-image problem, but apparenctly was not.
>
> Nubia P. Toman
> PhD student, Bioinformatics
> Universidade Federal de Minas Gerais
>
> ________________________________
> De: Carlos Simmerling <carlos.simmerling.gmail.com>
> Enviado: quinta-feira, 16 de abril de 2020 10:21
> Para: AMBER Mailing List <amber.ambermd.org>
> Assunto: Re: [AMBER] protein-protein complex dissociation
>
> Have you done a control on the wild type to see that it is more stable?
> Then you can have more confidence that the observation is due to the
> mutation.
>
> On Thu, Apr 16, 2020, 9:18 AM Núbia Toman <nnubiaits.hotmail.com> wrote:
>
> > 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
> >
> > [
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Received on Thu Apr 16 2020 - 07:30:02 PDT
