Thanks everyone for prompt response. I read amber16 manual and amber16 changelog page.
On Monday, January 2, 2017 8:20 AM, Elvis Martis <elvis.martis.bcp.edu.in> wrote:
HI,
Just to add to this, I have seen this behavior if you have zipped the NETCDF trajectory format then cpptraj and vmd could not process.
And in AMBER16 NETCDF Is the default trajectory format.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Nhai [mailto:nhai.qn.gmail.com]
Sent: Monday, January 02, 2017 9:27 PM
To: Saman Yousuf ali <saman.yousufali64.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] failed to visualize trajectories in vmd.
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 - 09:00:04 PST
