Carlos,
Thank you for your help. But I really do not know how to solve the imaging problem. So far I have been using:
parm .top
trajin .nc
reference ref.rst
strip :WAT,Na+,Cl- outprefix nowater
autoimage
center :1-330 origin
image origin center
rms reference :1-330
rms reference :1-330.CA,C,N nofit out .dat
Do you have any idea what else can be done?
Thanks,
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 13:51
Para: AMBER Mailing List <amber.ambermd.org>
Assunto: Re: [AMBER] protein-protein complex dissociation
if you see high RMSD and then low RMSD again, especially without a gradual
change in between, then it suggests an imaging problem. You might want to
visualize the entire trajectory to check.
On Thu, Apr 16, 2020 at 12:48 PM Núbia Toman <nnubiaits.hotmail.com> wrote:
> 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 - 10:30:02 PDT
