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 - 23:00:03 PST
