.Andy: (my shameless advertising) you can also use nglview (
https://github.com/arose/nglview) for trajectory viewer.
Since it uses cpptraj (via pytraj) as one of the backends for trajectory
parsing, you don't need to care about file format conversion.
feel free to open new issues on github page if you have any question.
cheers.
Hai
On Thu, Aug 4, 2016 at 6:31 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Amber 16 now has netcdf as a default for restart files. VMD is not able
> to read them at this time.
>
> You can try setting ntxo=1 in your mdin file or use cpptraj to read the
> restart file and use trajout to write it as ascii.
>
>
> adrian
>
>
>
> On 8/4/16 5:47 PM, macc_200 wrote:
> > I am using amber 16 on Ubuntu 14.04 LTS and attempting to follow the
> antechamber tutorial 4b.
> > http://ambermd.org/tutorials/basic/tutorial4b/ .
> >
> >
> > When I try to look at the crd file from the minimization step (min.in)
> using VMD (using the 1FKO_sus.prmtop file), it is unable to read the crd
> file. The error given is:
> > Using plugin crd for coordinates from file ...........Problem reading
> CRD file
> >
> > When I try to create a pdb from the minimized structure using the
> command ambpdb -p 1FKO_sus.prmtop ....... in the tutorial, it fails with
> the error
> > Error: Could not read restart atoms/time.
> > I was able to generate a pdb file within tleap using savepdb complex
> 1FKO_sus.pdb and this pdb read into VMD OK but it goes wrong after that.
> The jobs took a sensible amount of time to run and the relevant files are
> there.
> > Any idea what could be wrong?
> > thanks,Andy.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 04 2016 - 21:30:02 PDT
