From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Wed Mar 17 2021 - 12:45:15 CDT

>From my own experience, I think VMD for macOS 10.15 and later cannot yet load
NetCDF trajectories.
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32069.html

For the time being try converting the .nc file to .dcd file
using CPPTRAJ and see if that works.

Hope this helps,
Mortimer

On Wed, Mar 17, 2021 at 4:19 AM Prathit Chatterjee
<pc20apr_at_remove_yahoo.co.in> wrote:
>
> 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