If you are running interactively you need to type 'run' or 'go' to execute
any queued actions or analyses.
-Dan
On Wednesday, June 15, 2016, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
wrote:
> Ah, you are running in interactive mode. I never do that. I just
> create an input file and use -i.
>
> On Wed, 15 Jun 2016 15:42:40 +0200
> Batuhan Kav <bkav13.ku.edu.tr <javascript:;>> wrote:
>
> > Dear Hannes,
> >
> > I think I figured out what is going on. I don't get any output until I
> > quit cpptraj. Maybe this is how cpptraj works, honestly I don't recall
> > observing any behaviour like this before.
> >
> > After quitting cpptraj, all the output files contain the output.
> >
> > Batuhan
> >
> > On 06/15/16 15:11, Hannes Loeffler wrote:
> > > Hi Batuhan,
> > >
> > > it can't be totally empty. I have just used your masks with a test
> > > case of mine. None of your masks match anything in my system and
> > > what I get is
> > >
> > > # order parameters for masks :PA.C115 :PA.H15R :PA.H15S
> > > #Cn SCD_H1 sd(SCD_H1) SCD_H2 sd(SCD_H2)
> > > 1 nan -nan nan -nan
> > >
> > >
> > > What output do you get with
> > >
> > > cpptraj -p membrane_64_64_water.prmtop --mask ':PA.C115'
> > >
> > > this is just to make sure that your mask does match atoms in your
> > > system. Sorry, there is no check in the action routine if a mask
> > > amounts to 0 atoms.
> > >
> > >
> > > Cheers,
> > > Hannes.
> > >
> > >
> > > On Wed, 15 Jun 2016 14:23:28 +0200
> > > Batuhan Kav <bkav13.ku.edu.tr <javascript:;>> wrote:
> > >
> > >> Hi Hannes,
> > >>
> > >> cpptraj verison is v16.00.
> > >>
> > >> Sorry, I made a mistake in my explanation. The output file is
> > >> generated, yet it is empty. I confused the wording, sorry.
> > >>
> > >> Batuhan
> > >>
> > >> On 06/15/16 13:13, Hannes Loeffler wrote:
> > >>> I can't tell what is wrong here. An output should always be
> > >>> created at the end when cpptraj runs the lipidorder action
> > >>> successfully.
> > >>>
> > >>> What version of cpptraj are you using? Make sure you have the
> > >>> most recent one from AmberTools16.
> > >>>
> > >>>
> > >>> On Wed, 15 Jun 2016 12:24:49 +0200
> > >>> Batuhan Kav <bkav13.ku.edu.tr <javascript:;>> wrote:
> > >>>
> > >>>> Dear Hannes,
> > >>>>
> > >>>> This is the output cpptraj gives;
> > >>>>
> > >>>> Konsole output
> > >>>> ---------- RUN BEGIN
> > >>>> -------------------------------------------------
> > >>>>
> > >>>> PARAMETER FILES (1 total):
> > >>>> 0: membrane_64_64_water.prmtop, 38128 atoms, 7376 res, box:
> > >>>> Orthogonal, 7120 mol, 6992 solvent
> > >>>>
> > >>>> INPUT TRAJECTORIES (1 total):
> > >>>> 0: 'test_ai_centered.mdcrd' is a NetCDF AMBER trajectory, Parm
> > >>>> membrane_64_64_water.prmtop (Orthogonal box) (reading 6000 of
> > >>>> 6000) Coordinate processing will occur on 6000 frames.
> > >>>>
> > >>>> BEGIN TRAJECTORY PROCESSING:
> > >>>> .....................................................
> > >>>> ACTION SETUP FOR PARM 'membrane_64_64_water.prmtop' (1 actions):
> > >>>> 0: [lipidorder out orderout z scd ":PA.C115" ":PA.H15R"
> > >>>> ":PA.H15S"] ----- test_ai_centered.mdcrd (1-6000, 1) -----
> > >>>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> > >>>>
> > >>>> Read 6000 frames and processed 6000 frames.
> > >>>> TIME: Avg. throughput= 2409.3328 frames / second.
> > >>>>
> > >>>> ACTION OUTPUT:
> > >>>>
> > >>>> DATAFILES (1 total):
> > >>>> orderout (Lipid order, Lipid order, Lipid order)
> > >>>>
> > >>>> RUN TIMING:
> > >>>> TIME: Init : 0.0000 s ( 0.00%)
> > >>>> TIME: Trajectory Process : 2.4903 s (100.00%)
> > >>>> TIME: Action Post : 0.0000 s ( 0.00%)
> > >>>> TIME: Analysis : 0.0000 s ( 0.00%)
> > >>>> TIME: Data File Write : 0.0000 s ( 0.00%)
> > >>>> TIME: Other : 0.0000 s ( 0.00%)
> > >>>> TIME: Run Total 2.4904 s
> > >>>> ---------- RUN END
> > >>>> ---------------------------------------------------
> > >>>>
> > >>>> In the end, no orderout file is created.
> > >>>>
> > >>>> Batuhan
> > >>>>
> > >>>> On 06/15/16 12:19, Hannes Loeffler wrote:
> > >>>>> On Wed, 15 Jun 2016 11:56:31 +0200
> > >>>>> Batuhan Kav <bkav13.ku.edu.tr <javascript:;>> wrote:
> > >>>>>
> > >>>>>> Dear All,
> > >>>>>>
> > >>>>>> I simulated a POPC bilayer and now want to calculate the lipid
> > >>>>>> order parameters using lipidorder command in AmberTools16.
> > >>>>>>
> > >>>>>> I give this command
> > >>>>>>
> > >>>>>> Konsole output
> > >>>>>> parm membrane.prmtop
> > >>>>>> trajin traj.mdcrd
> > >>>>>> lipidorder out orderout z scd ":PA.C115" ":PA.H15R" ":PA.H15S"
> > >>>>>> run
> > >>>>>>
> > >>>>>> to calculate the order parameter for C115 (second from the last
> > >>>>>> of the PA tail). cpptraj works without producing any errors,
> > >>>>>> yet it doesn't produce any outputs. That is, orderout file is
> > >>>>>> not created.
> > >>>>> cpptraj writes information on what it does on stdout. What does
> > >>>>> it say? Is suspect your masks may not be balanced i.e. the
> > >>>>> three masks do not contain exactly the same number of atoms.
> > >>>>>
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--
-------------------------
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/
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Received on Wed Jun 15 2016 - 07:30:02 PDT
