Carlos,
I visualized the entire trajectory generated with the previous command. For most of the simulation time, I did not see any imaging problem, just for few frames (79). Considering that its an imaging issue, how could it be solved?
Thank you,
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 14:12
Para: AMBER Mailing List <amber.ambermd.org>
Assunto: Re: [AMBER] protein-protein complex dissociation
I think the important thing is to add a trajout command at the end, and
then visually check that new trajectory in a program like VMD. don't worry
about solving the problem until you know it exists...
On Thu, Apr 16, 2020 at 1:04 PM Núbia Toman <nnubiaits.hotmail.com> wrote:
> 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 - 11:00:03 PDT
