Thanks Danie,
it worked exactly as you said.
On Fri, Jun 6, 2014 at 7:23 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 560012*
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Received on Sat Jun 07 2014 - 05:30:02 PDT
