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> 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> 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> 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> 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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Received on Wed Jun 15 2016 - 07:30:02 PDT
