Cpptraj can read, process, and write many coordinate formats
(including restart and PDB files). For a full listing of supported
formats, consult the manual. Also, I recommend giving 'autoimage' a
try instead of center/image.
-Dan
On Wed, Sep 24, 2014 at 8:38 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> Dear Amber users!
>
> I wounder to ask whether it possible to remove periodicity and center the
> protein within the box having only restart file (no trajectory) with the
> lattest coordinates as the input
>
> typically I do it using the following tleap script:
>
> trajin md.nc 1 last 5
> reference protein.inpcrd
> center :1-289 mass origin
> image origin center
> rms reference :1-361.CA out rmsd.dat
> trajout md_proc.nc netcdf nobox
>
> is it possible to do the same task using only .inpcrd file as the input and
> to obtain output as the pdb in any pptraj one-script method?
>
> Thanks for help,
>
> James
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Sep 24 2014 - 08:00:03 PDT
