Hi,
It would be more useful if I could actually see what the issue is. Can
you send me off-list the topology and a few frames that illustrate the
problem you are having? Thanks,
-Dan
On Wed, Oct 7, 2020 at 3:12 AM Suchetana Gupta <tutulg.gmail.com> wrote:
>
> 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 - 08:00:04 PDT
