VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Wed Dec 18 2019 - 07:25:11 CST

Dear all,

Did VMD change the netcdf plugin between version 1.9.4a12 and 1.9.4a38 ?
I am using netcdf trajectories created with CPPTRAJ program from
AmberTools 19.

When I load these trajectories in VMD 1.9.4a12, everything works well ....

However, with VMD 1.9.4a38, I cannot load exactly the same trajectories
loaded correctly with the a12 version. I am getting the error below. I
will revert for now to the a12 version, but maybe this is worth
investigating.

Best wishes
Vlad

netcdfplugin) conventions: 'AMBER'
netcdfplugin) trajectory follows AMBER conventions version '1.0'
netcdfplugin) AMBER: program 'cpptraj'
netcdfplugin) AMBER: program version 'V18.01'
netcdfplugin) AMBER: title 'Cpptraj Generated trajectory'
netcdfplugin) AMBER: application 'AMBER'
netcdfplugin) AMBER: spatial dimension: 3
netcdfplugin) AMBER: atom dimension: 13042
netcdfplugin) AMBER: frame dimension: 80000
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 ../test.ncdf
vmd_LINUXAMD64: putget.c:3593: getNCvx_float_float: Assertion `value !=
((void *)0)' failed.
Abort (core dumped) 

-- 
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru