Sorry, I didn't read the original email closely enough. If you want to
remove periodicity completely after centering the protein then yes you
should add the 'unwrap' option after 'autoimage'. If you want things
centered explicitly at the origin specify the 'origin' keyword to
'autoimage'.
-Dan
On Thu, Sep 25, 2014 at 1:52 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> 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
--
-------------------------
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 Thu Sep 25 2014 - 08:30:02 PDT
