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 - 07:00:03 PDT
