Hi,
First, I recommend upgrading to AmberTools 14. Second, if you're
trying to read a netcdf trajectory with only velocities in it (or you
want to use velocities instead of coordinates in a combined crd/vel
netcdf file) you need to specify 'usevelascoords' on the trajin line,
e.g. 'trajin mdvel 1 10000 usevelascoords'. This option also works for
netcdf restarts. I have just noticed that this option is not yet
documented in the manual, but it is present in version 14 of cpptraj.
Hope this helps,
-Dan
On Fri, Jun 6, 2014 at 5:00 AM, Himanshu Joshi <himanshuphy87.gmail.com> wrote:
> Dear friends,
>
> I tried cpptraj to convert an amber md velocity file from
> binary (netcdf) to ascii format. It gave me the following error saying
>
> *NETCDF Error: NetCDF: Variable not found...*
>
> If anyone has any comment or suggestion regarding this,
> please share with me.
>
>
>
> *here are the details of the error output..*
>
>
>
>
> cpptraj ../../parm/66_49nm_40.prmtop <ptraj.in
>
> CPPTRAJ: Trajectory Analysis. V13.1
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> AmberParm Title: [DEN]
> Radius Set: modified Bondi radii (mbondi)
> INPUT: Reading Input from STDIN
> [trajin mdvel 1 10000]
> [mdvel] contains 10000 frames.
> Warning: Box information present in parm but not in trajectory.
> Warning: DISABLING BOX in parm [66_49nm_40.prmtop]!
> [trajout mdvel_asc.trj vel]
>
> PARAMETER FILES:
> 0: 66_49nm_40.prmtop, 171597 atoms, 55600 res, box: None, 55600 mol, 55599
> solvent, 10000 frames
>
> INPUT TRAJECTORIES:
> 0: [mdvel] is a NetCDF AMBER trajectory containing velocities, Parm
> 66_49nm_40.prmtop (reading 10000 of 10000)
> Coordinate processing will occur on 10000 frames.
>
> REFERENCE COORDS:
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> [mdvel_asc.trj] is an AMBER trajectory, Parm 66_49nm_40.prmtop: Writing
> 10000 frames (1-Last, 1)
>
> BEGIN TRAJECTORY PROCESSING:
> ----- [mdvel] (1-10000, 1) -----
> 0% NETCDF Error: NetCDF: Variable not found
> Error: Getting frame 0
>
> Read 0 frames and processed 0 frames.
>
> ACTION OUTPUT:
>
> DATASETS:
> No data sets.
>
>
>
> Thanks
> --
>
>
>
> *With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
> TheoryDepartment of Physics IISc.,Bangalore India 560012*
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jun 06 2014 - 07:00:02 PDT
