Hi, Carlos
Actually, as I was looking at reduced trajectory I did no see these jumps on RMSD values. Now that I am looking at the entire trajectory I see high RMSD values for some frames (from frame 29123 to 29202, of 50000 frames), even after all aligning and image process.
Best,
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 11:09
Para: AMBER Mailing List <amber.ambermd.org>
Assunto: Re: [AMBER] protein-protein complex dissociation
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 - 10:00:02 PDT
