Can you try cpptraj in amber16? Yours is v15.
Hai Nguyen
> On Jan 2, 2017, at 10:46 AM, Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
>
> Okay, I have finally tried to re-image my unzipped file, input script and result is pasted below
>
> gunzip -9 *.gz
> reimage.in========parm file.prmtop
> trajin md_simulation1.mdcrd
> trajin md_simulation2.mdcrd
> center :1-672 mass origin
> image origin familiar
> trajout md_simulation1-2ns.mdcrd
> output=======zuh.node15:~/Working/test-md/prod> cpptraj -i reimage.in
>
> CPPTRAJ: Trajectory Analysis. V15.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 01/03/17 04:34:20
> | Available memory: 4129.16 MB
>
> INPUT: Reading Input from file reimage.in
> [parm ../file.prmtop]
> Reading '../file.prmtop' as Amber Topology
> [trajin md_simulation1.mdcrd]
> Reading 'md_simulation1.mdcrd' as Amber NetCDF
> [trajin md_simulation2.mdcrd]
> Reading 'md_simulation2.mdcrd' as Amber NetCDF
> [center :1-672 mass origin]
> CENTER: Centering coordinates using center of mass of atoms in mask (:1-672) to
> coordinate origin.
> [image origin familiar]
> IMAGE: By molecule to origin based on first atom position using atoms in mask *
> Triclinic On, familiar shape.
> [trajout md_simulation1-2ns.mdcrd]
> Warning: Format not specified and extension '.mdcrd' not recognized. Defaulting to Amber Trajectory.
> Writing 'md_simulation1-2ns.mdcrd' as Amber Trajectory---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES:
> 0: '4KIK-KSA.prmtop', 186986 atoms, 59360 res, box: Orthogonal, 58690 mol, 58680 solvent, 2000 frames
>
> INPUT TRAJECTORIES:
> 0: 'md_simulation1.mdcrd' is a NetCDF AMBER trajectory, Parm file.prmtop (Orthogonal box) (reading 1000 of 1000)
> 1: 'md_simulation2.mdcrd' is a NetCDF AMBER trajectory, Parm file.prmtop (Orthogonal box) (reading 1000 of 1000)
> Coordinate processing will occur on 2000 frames.
>
> OUTPUT TRAJECTORIES:
> 'md_simulation1-2ns.mdcrd' is an AMBER trajectory, Parm file.prmtop: Writing 2000 frames (1-Last, 1)
> TIME: Run Initialization took 0.0001 seconds.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'file.prmtop' (2 actions):
> 0: [center :1-672 mass origin]
> Mask [:1-672] corresponds to 10938 atoms.
> 1: [image origin familiar]
> Number of molecules to be imaged is 58690 based on mask '*'
> ----- md_simulation1.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90%100% Complete.----- md_simulation2.mdcrd (1-1000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90%100% Complete To avoid this error in future,Can you please explain me the exact problem?
>
>
> On Monday, January 2, 2017 7:32 AM, Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
>
>
> Yes, I am sure. It was mdcrd.gz (binary file) and I have unzip this file using gunzip -9 md_simulation1.mdcrd.gz command.
>
>
> On Monday, January 2, 2017 7:20 AM, David Case <david.case.rutgers.edu> wrote:
>
>
>> On Mon, Jan 02, 2017, Saman Yousuf ali wrote:
>>
>> [trajin md_simulation1.mdcrd.gz]
>> Error: Could not determine trajectory md_simulation1.mdcrd.gz format.
>
> Something is wrong with your trajin file. How did you create it? Are you
> sure it is indeed a gzipped file? (Try using 'gunzip' on this file).
>
> There is something wrong with this file (since both VMD and cpptraj cannot
> process it), but it is going to be difficult to debug the problem remotely.
>
> ....dac
>
>
>
>
>
>
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Received on Mon Jan 02 2017 - 08:00:03 PST
