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.
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 15 2016 - 05:30:02 PDT
