Yes Dr. Anselm
This is what I used for my imaging file:
trajin 6md.cdf
strip :WAT
unwrap
autoimage
rms first :1-754.C,CA,N
trajout imaged6.nc netcdf
I do notice those jumps in RMSD in between for some frames.
Thanks
Suchetana
On Wed, Oct 7, 2020 at 12:39 PM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Dear Suchetana,
>
> just to be sure about that:
> - You did use iwrap=1 in your simulation and observe such "dissociation"
> (visible as instantaneous RMSD jumps in the RMSD plot), right?
> - You tried to strip the solvent, unwrap the protein trajectory and fit
> onto the first frame, which resembles the correct system?
> - How does your RMSD plot look like? Did you observe "dissociation"
> events again? Did you visualize the trajectory?
>
> Since you already simulated some time, it would be annoying to re-do all
> that...
>
> Regards,
>
> Anselm
>
>
> On 10/07/2020 08:56 AM, Suchetana Gupta wrote:
> > Thank you Dr. Anselm for the response. I have tried these options too.
> > Unwrap also did not work. I resimulated by keeping irest=0, ntx=1. For
> > those trajectories, the imaging issue was less. However for some frames,
> > the same issues did persist. Then I saw another post where it was
> > suggested to keep iwrap=0. I am trying with that option now.
> > Thanks
> > Suchetana
> >
> > On Wed, Oct 7, 2020 at 12:18 PM Dr. Anselm Horn <anselm.horn.fau.de
> > <mailto:anselm.horn.fau.de>> wrote:
> >
> > Dear Suchetana,
> >
> > this issue has been raised and addressed repeatedly on this list.
> > I suggest to unwrap the trajectory in order to neutralize the effect
> of
> > iwrap=1 in your input.
> >
> > Please try out something like
> >
> > # Strip water to avoid computational burden
> > strip :WAT
> > # Unwrap the protein system,
> > # i.e. counter the original imaging during the simulation
> > unwrap
> > # Add image commands for ions if interested;
> > # otherwise they could be stripped together with the solvent.
> > # Fit on first structure
> > rms first :1-754.C,CA,N
> > # Output commands follow ...
> >
> > but have a look into the manual about the correct syntax of the
> > commands.
> >
> > Regards,
> >
> > Anselm
> >
> > On 10/07/2020 06:43 AM, Suchetana Gupta wrote:
> > > Dear all
> > > I simulated a protein-protein complex using Amber20 for 100ns. The
> > system
> > > consists of a dimer complexed with two copies of the same protein.
> > I used a
> > > cubic water box. When I ran autoimage using AmberTools18, till
> > ~50ns, the
> > > trajectory is fine. However, beyond that, there seems to be some
> > imaging
> > > issues. I am just not able to solve this.
> > > Can someone please help me?
> > >
> > > The input files that I have tried are:
> > >
> > > Trial1
> > > trajin 6md.cdf
> > > autoimage
> > > trajout imaged6.nc <http://imaged6.nc> netcdf
> > >
> > > Trial2
> > > trajin 6md.cdf
> > > autoimage
> > > trajout imaged6.nc <http://imaged6.nc> netcdf nobox
> > >
> > >
> > > Trial3
> > > trajin 6md.cdf
> > > center :1-199 origin mass
> > > image origin center
> > > center :1-398 origin mass
> > > image origin center
> > > center :1-576 origin mass
> > > image origin center
> > > image origin center
> > > center :1-754
> > > trajout imaged6.nc <http://imaged6.nc> netcdf
> > > (1-199 is one monomer of protein1, 200 to 398 is monomer 2 of
> > protein 1,
> > > 399 to 576 and 577 to 754 are the two copies of the partner
> protein)
> > >
> > > Thanks
> > > Suchetana Gupta
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
>
>
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Received on Wed Oct 07 2020 - 00:30:02 PDT
