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> 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 netcdf
> >
> > Trial2
> > trajin 6md.cdf
> > autoimage
> > trajout 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 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
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Wed Oct 07 2020 - 00:00:02 PDT
