Re: [AMBER] failed to visualize trajectories in vmd.

From: Saman Yousuf ali <>
Date: Mon, 2 Jan 2017 15:08:41 +0000 (UTC)

Thanks David for answering my queries. I have unzipped mdcrd file before loading in vmd. I have also re-imaged these trajectories file using following cpptraj script; file.prmtop
trajin md_simulation1.mdcrd.gz
trajin md_simulation2.mdcrd.gz
center :1-672 mass origin
image origin familiar
trajout netcdf
and got error
zuh.node15:~/Working/test-md/prod> cpptraj -i

CPPTRAJ: Trajectory Analysis. V15.00
    ___  ___  ___  ___
     | \/ | \/ | \/ |

| Date/time: 01/03/17  03:59:13
| Available memory: 2983.8 MB

INPUT: Reading Input from file
  [parm file.prmtop]
        Reading 'file.prmtop' as Amber Topology
  [trajin md_simulation1.mdcrd.gz]
Error: Could not determine trajectory md_simulation1.mdcrd.gz format.
Error: Could not set up input trajectory 'md_simulation1.mdcrd.gz'.
        1 errors encountered reading input.
TIME: Total execution time: 0.8559 seconds.
Any suggestion on how to fix this issue?


    On Monday, January 2, 2017 6:14 AM, David Case <> wrote:

 On Mon, Jan 02, 2017, Saman Yousuf ali wrote:

> Dear all,We have currently switched from amber14 to amber16.

The default output for restart files was changed in amber16, to netcdf format.
If you wish to get the old format, set ntxo=1.

> After 3ns, I tried to use ambpdb command  to check the result, but I got
> following error message;| ambpdb (C++) Version V15.00

Of courese, if you are using Amber16, you should also use AmberTools16.  The
ambpdb program can accept netcdf restart files, using the "-c" flag.

> Now the issue is I cannot see thetrajectories (mdcrd.gz file) using
> VMD. Could anybody let me know what went wrong? 

Not without more information.  At a minimum, we would need to know the exact
symptoms, i.e. what input did you give to VMD, and what messages did it emit?

Nothing has changed about trajectory files in Amber for a very long time.
We recommend that you use ioutfm=1 to get netcdf format for trajectories:
there are many reasons for this, and VMD understands them fine.  Are
you sure VMD knows how to gunzip the old formatted files internally?
Suggestion: use cpptraj to examine your trajectory file, making sure it
seems to be OK and have the expected number of frames.  Try VMD with the
unzipped file.


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Received on Mon Jan 02 2017 - 07:30:02 PST
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