Hi,
The 'fixatomorder' command is an action; when you run cpptraj interactively
typing an action command adds it to the 'Action List' - actions in the list
are not performed until you execute a 'run' command, after which actions
are performed on frames read in from prior 'trajin' commands. You can see
what actions/trajectories/etc you have currently loaded with the 'list'
command. The commands you should issue (assuming your topology is named
ionicbox.prmtop and your input coordinates are named ionicbox.inpcrd) are:
cpptraj -p ionicbox.prmtop
> trajin ionicbox.inpcrd
> fixatomorder outprefix fixed
> trajout fixed.ionicbox.inpcrd
> run
The 'outprefix' keyword will print a re-ordered topology named
fixed.ionicbox.prmtop, and the output trajectory fixed.ionicbox.inpcrd will
contain the re-ordered coordinates. Hope this helps,
-Dan
On Sat, Mar 8, 2014 at 2:42 AM, Saeed Nasiri <s.t.nasiri.gmail.com> wrote:
> Dear Jason
> Thanks for good commands, but I can't anything about fixatomorder. I did
> the following things with cpptraj, but I don't know they are true or no? I
> attached the new and old prmtop files but I can't write the coordinate file
> (incprd).
> Also this system is similar to amber ionic liquid simulation tutorial.
>
> Your Sincerely
> Nasiri
>
>
> =================================================================================
>
> cpptraj -p ionicbox.prmtop
>
> CPPTRAJ: Trajectory Analysis. V13.22
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> AmberParm Title: [default_name]
> Radius Set: modified Bondi radii (mbondi)
>
> > fixatomorder
> FIXATOMORDER: Will attempt to fix atom ordering when atom numbering
> in molecules is non-sequential.
> > parmwrite out ionicbox2.prmtop
> Writing parm 0 (ionicbox.prmtop) to Amber parm ionicbox2.prmtop
> > average ionicbox2.inpcrd
> AVERAGE: Averaging over coordinates in mask [*]
> Start: 1 Stop: Final frame
> Writing averaged coords to [ionicbox2.inpcrd]
> >
>
> =====================================================================
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Sat Mar 08 2014 - 08:30:03 PST
