VMD-L Mailing List

From: viktor drobot (linux776_at_gmail.com)
Date: Sun Sep 15 2019 - 08:43:38 CDT

Hello, VMD developers! After some update (don't remember exactly what
version it was, but I think around 1.9.4 alpha-31) VMD doesn't read
plaintext mdcrd trajectories of AMBER (I use version 18) but works with
NetCDF format.

Here are output of loading topology + NetCDF trajectory in VMD 1.9.4a37:
vmd > Info) Using plugin parm7 for structure file /tmp/1/system.prmtop
Info) Analyzing structure ...
Info)    Atoms: 85722
Info)    Bonds: 85764
Info)    Angles: 0  Dihedrals: 0  Impropers: 0 Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0 Impropertypes: 0
Info)    Residues: 25433
Info)    Waters: 24540
Info)    Segments: 1
Info)    Fragments: 24671   Protein: 2   Nucleic: 0
netcdfplugin) conventions: 'AMBER'
netcdfplugin) trajectory follows AMBER conventions version '1.0'
netcdfplugin) AMBER: program 'pmemd'
netcdfplugin) AMBER: program version '16.0'
netcdfplugin) AMBER: title 'default_name'
netcdfplugin) AMBER: application 'AMBER'
netcdfplugin) AMBER: spatial dimension: 3
netcdfplugin) AMBER: atom dimension: 85722
netcdfplugin) AMBER: frame dimension: 300
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 /tmp/1/heat.nc
Info) Coordinate I/O rate 60.2 frames/sec, 59 MB/sec, 5.0 sec
Info) Finished with coordinate file /tmp/1/heat.nc.

Trajectory is read successfully, I can see total number of frames and
visual representation. However, it's not true for plaintext mdcrd format:
vmd > Info) Using plugin parm7 for structure file /tmp/1/system.prmtop
Info) Analyzing structure ...
Info)    Atoms: 85722
Info)    Bonds: 85764
Info)    Angles: 0  Dihedrals: 0  Impropers: 0 Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0 Impropertypes: 0
Info)    Residues: 25433
Info)    Waters: 24540
Info)    Segments: 1
Info)    Fragments: 24671   Protein: 2   Nucleic: 0

Neither "AMBER Coordinates", nor "AMBER Coordinates with Periodic Box"
doesn't work - there are no visual representation, no output in console
and I can see only 0 frames.

Does plain AMBER trajectories are still supported?