Hi Dan,
using just
autoimage
trajout md_proc.nc netcdf nobox
have produced trajectory still having periodicity in Y dimension
should I add something else like \unwrap\ option?
Best,
James
2014-09-24 16:42 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 25 2014 - 01:00:03 PDT
