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
> > > >
> > > > [
> > > >
> > >
> >
> https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif
> > > > ]<
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon
> > > >
> > > > Virus-free. www.avast.com<<http://www.avast.com<>
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > [
> > >
> >
> https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif
> > > ]<
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon
> > >
> > > Virus-free. www.avast.com<<http://www.avast.com<>
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > [
> >
> https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif
> > ]<
> >
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon
> >
> > Virus-free. www.avast.com<<http://www.avast.com<>
> >
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> [
> https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif
> ]<
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon>
> Virus-free. www.avast.com<
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 16 2020 - 10:30:02 PDT
