I think there's a misunderstanding of what "trajout" does, which is mostly
inherited from the ptraj way of doing things. There is only _one_
"trajout" action that takes place, and it takes place after every other
action is done.
The original (ptraj) workflow (simplified) was this:
1) read in trajectories
2) Do a bunch of things to that trajectory (which may just be passive
measurements or actions that modify those coordinates, such as RMS-fitting,
stripping, etc.)
3) Write out a new trajectory modified by all of the actions in 2).
Therefore, what is happening is that each time you issue a new 'trajout'
command to cpptraj, it overwrites the one that came before. (Also, no
actions are actually executed until you type 'go' or Ctrl-D, which is EOF
in Unix)
Dan did add a trajectory output action that keeps its place in the action
stack (and can therefore be specified numerous times), called "outtraj".
If you replace the "trajout" command with "outtraj" commands (the rest of
the arguments are the same), that should give you the behavior you want.
Note, though, that while trajout will write the same frames in the same
way regardless of where it is specified, the trajectory printed by
'outtraj' will depend on where it appears in the list of actions.
HTH,
Jason
On Sun, Feb 10, 2013 at 4:19 PM, Jonathan Saboury <jsabou1.gmail.com> wrote:
> Sorry for the lack of details, thought I was overkilling it before.
>
> Here are the commands I did to try to make it output:
> http://pastebin.com/raw.php?i=GF6iupZt
>
> the pdb is the output from openmm
>
> Thanks!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Feb 10 2013 - 15:00:02 PST
