Try using the vmd flags. Like this:
vmd -parm7 *prmtop file* -netcdf *trajectory file*
Rashid
On Wed, Dec 6, 2017 at 3:11 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> I'd try the plain Amber coordinates option, just in case. I forget how I
> solved this, but I complained as high up the VMD food chain as I could
> about the lack of a useful error message.
>
> Is the mdcrd readable and non-0 in size?
>
> Bill
>
>
> On 12/5/17 10:57 PM, Biplab Ghosh wrote:
> > Dear Amber Users,
> >
> > I am simulation a protein-ligand complex using Amber16 and using
> vmd-1.9.3
> > for visualization of trajectories.
> >
> > I am following the method described in one of the Amber tutorials for
> using
> > vmd for visualizing the trajectories, but getting the following error:
> >
> > Info) Using plugin crdbox for coordinates from file
> > /home1/biplab/Amber-Simulation/pcpdr-sub/prod-md.mdcrd
> > Problem reading CRD file
> > Info) Finished with coordinate file
> > /home1/biplab/Amber-Simulation/pcpdr-sub/prod-md.mdcrd.
> >
> > First I loaded the prmtop file in vmd andgot the following output in the
> > terminal:
> >
> > vmd > Info) Using plugin parm7 for structure file
> > /home1/biplab/Amber-Simulation/pcpdr-sub/pcpdr-PCA.prmtop
> > Info) Analyzing structure ...
> > Info) Atoms: 94950
> > Info) Bonds: 95134
> > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > Info) Residues: 28298
> > Info) Waters: 27448
> > Info) Segments: 1
> > Info) Fragments: 27456 Protein: 8 Nucleic: 0
> >
> > Then I loaded the mdcrd file with the filetype "Amber coordinates with
> > periodic box".
> >
> > Can anyone please help me in resolving the err: "Problem reading CRD
> file" ?
> >
> > With regards
> > Biplab.
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Dec 06 2017 - 00:00:02 PST
