On Fri, Sep 19, 2014 at 7:29 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
> Try using the "fixatomorder" command at the beginning of your cpptraj
> script. That should fix the molecule issue and allow you to image.
>
> Note that you should write a new prmtop file since the atom ordering in
> your system will change (and you will need this new prmtop file to analyze
> any trajectory you print out after running fixatomorder).
Just to add to this, you can use the 'outprefix' keyword with
'fixatomorder' (similar to the 'strip' command) to write out a
re-ordered topology file that will match re-ordered coordinates.
-Dan
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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
Received on Fri Sep 19 2014 - 07:00:03 PDT
