Do not select "amber coordinates with periodic condition" option. After
loading parameter file, load the netcdf file as "automatically file type"
On Saturday, September 24, 2016, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > Problem reading CRD file
>
> One possible cause is your md run terminated abnormally, and the file
> wasn't closed properly.
>
> Bill
>
>
> On 9/24/16 1:39 PM, Andrew Bostick wrote:
> > Dear Daniel and David,
> >
> > Thanks for your answers. I did what you suggested to obtain trajectory
> file
> > as netcdf.
> >
> > To visualize the trajectory file using VMD 1.9, I loaded *.prmtop at
> first
> > then I loaded *.netcdf files with amber coordinates with periodic box.
> But
> > VMD did not show any thing in OpenGL window:
> >
> > vmd > Info) Using plugin parm7 for structure file
> > C:/Users/baharrayane/Desktop/test/comp_sol.prmtop
> > Info) Analyzing structure ...
> > Info) Atoms: 26383
> > Info) Bonds: 26400
> > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > Info) Residues: 8250
> > Info) Waters: 8119
> > Info) Segments: 1
> > Info) Fragments: 8128 Protein: 1 Nucleic: 0
> > Info) Using plugin crdbox for coordinates from file
> > C:/Users/baharrayane/Desktop/test/density.netcdf
> > Problem reading CRD file
> > Info) Finished with coordinate file
> > C:/Users/baharrayane/Desktop/test/density.netcdf.
> >
> > What is the reason of this issue?
> >
> > Any help will highly be appreciated.
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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--
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Received on Sat Sep 24 2016 - 23:30:02 PDT
