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 - 03:30:03 PDT
