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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 15 2016 - 04:30:02 PDT
