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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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 26 2015 - 06:00:04 PDT
