I am really thankful for your help prof. Swails, It works successfully !
On Fri, Jun 26, 2015 at 2:40 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Jun 26, 2015 at 7:17 AM, Hadeer ELHabashy <
> hadeer.elhabashi.gmail.com> wrote:
>
> > Dear sir
> >
> > wish you are fine !
> >
> > I want to align about 1000 .rst7 frames of a protein to the first frame
> > into one .crd file in order to create a movie with VMD, I tried many
> > cpptraj commands as the following but the protein keeps jumping or
> > rotating or trans-locateing in the created movies .
> > I will be so grateful for you if you advice me with the right command to
> do
> > so.
> >
>
> When I'm trying to prepare a trajectory for visualization, I usually do
> something like
>
> trajin mol0.rst7
> trajin mol1.rst7
> ...
> trajin mol1000.rst7
>
> autoimage
> rmsd mol_rmsd @CA,C,N first
>
> trajout imaged.nc
>
> The above command will create a NetCDF trajectory, imaging everything into
> a single unit cell (with the first solute molecule at the center of that
> cell), align to the protein backbone of the first structure (which is
> mol0.rst7), and then print the new trajectory. This is all slightly
> different from your examples below, but your description suggests an
> imaging artifact that will be fixed with the "autoimage" command.
>
> HTH,
> Jason
>
>
>
> >
> >
> > trajin mol0.rst7
> > ...
> > trajun mol1000.rst7
> > reference mol0.rst7
> > rms reference 1 175
> > trajout all_frames.crd
> >
> > &
> >
> > trajin mol0.rst7
> > ...
> > trajun mol1000.rst7
> > center:1
> > trajout all_frames.crd
> >
> > &
> >
> > trajin mol0.rst7
> > ...
> > trajun mol1000.rst7
> > unwrap
> > trajout all_frames.crd
> >
> >
> > Best Regards
> > Hadeer ELHabashy
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Fri Jun 26 2015 - 07:00:03 PDT
