Hi,
You cannot read or write compressed NetCDF trajectories - see the
table in the Amber 16 manual, cpptraj section '29.8 Trajectory File
Commands'.
-Dan
On Mon, Jan 2, 2017 at 11:59 AM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Jan 03 2017 - 06:00:02 PST
