VMD-L Mailing List

From: Prathit Chatterjee (pc20apr_at_REMOVE_yahoo.co.in)
Date: Wed Mar 17 2021 - 03:03:39 CDT

Dear VMD experts,
I am unable to open a .nc file in my VMD (VMD for MACOSXX86_64, version 1.9.4a51 (December 21, 2020)) installed in MAC  OS (BigSur 11.2.3),even mentioning the filetype in the command:
vmd > Info) Using plugin parm7 for structure file /Users/prathitchatterjee/APP-trial/APP-2000th-frame/step5_input.parm7
Info) Analyzing structure …
Info) Atoms: 2207705
Info) Bonds: 2202780
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 659910
Info) Waters: 652583
Info) Segments: 1
Info) Fragments: 657889 Protein: 5 Nucleic: 0

vmd > mol addfile step6.1_equilibration.nc -netcdf waitfor all
Could not determine file type for file 'step6.1_equilibration.nc' from its extension.
vmd > mol addfile step6.1_equilibration.nc type netcdf waitfor all
ERROR) Cannot read file of type netcdf
Unable to load file 'step6.1_equilibration.nc' using file type 'netcdf'.

 However, I could do so in my linux based server as follows (VMD for LINUXAMD64, version 1.9.4a51 (December 21, 2020)):
vmd > mol new step5_input.parm7
Info) Using plugin parm7 for structure file step5_input.parm7
Info) Analyzing structure ...
Info) Atoms: 2207705
Info) Bonds: 2202780
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 659910
Info) Waters: 652583
Info) Segments: 1
Info) Fragments: 657889 Protein: 5 Nucleic: 0
0
vmd > mol addfile step6.1_equilibration.nc waitfor all
netcdfplugin) conventions: 'AMBER'
netcdfplugin) trajectory follows AMBER conventions version '1.0'
netcdfplugin) AMBER: program 'pmemd'
netcdfplugin) AMBER: program version 'Version 20'
netcdfplugin) AMBER: application 'AMBER'
netcdfplugin) AMBER: spatial dimension: 3
netcdfplugin) AMBER: atom dimension: 2207705
netcdfplugin) AMBER: frame dimension: 25
netcdfplugin) AMBER: coordinates units: 'angstrom'
netcdfplugin) AMBER: no coordinates scalefactor attribute, 1.0 assumed
netcdfplugin) AMBER: coordinates scalefactor: 1.000000
netcdfplugin) AMBER trajectory contains periodic cell information
netcdfplugin) AMBER: cell lengths units: 'angstrom'
netcdfplugin) AMBER: no cell lengths scalefactor attribute, 1.0 assumed
netcdfplugin) AMBER: cell lengths scalefactor: 1.000000
netcdfplugin) AMBER: cell angles units: 'degree'
netcdfplugin) AMBER: no cell angles scalefactor attribute, 1.0 assumed
netcdfplugin) AMBER: cell angles scalefactor: 1.000000
Info) Using plugin netcdf for coordinates from file step6.1_equilibration.nc
Info) Finished with coordinate file step6.1_equilibration.nc.
0

I also could not find any suitable file format selection type as well to load the .nc format in the graphics version of MAC installed VMD.
Any suggestions regarding resolving the same will be deeply appreciated.
Sincerely,Prathit Chatterjee