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 - 06:30:03 PDT
