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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Received on Tue Dec 05 2017 - 23:30:03 PST
