> Amber ptraj has a utitlity for converting mdcrd files to netcdf binary
> format. I tried it and I thought it
> was successful. However there is this program called nMOLDYN which
> reads only netcdf format.
> I tried to read this converted trajectory in nMOLDYN and it says that
> this maynot be a trajectory.
> Has anyone tried using this software or the netcdf format.
Unlike ascii (which is a character standard), netCDF is a generic,
extensible, machine independent, pseudo-annotated and binary file format
*specification* that can be adapted to store different types of data.
Think of it as a language for specifying a file format; each instantiation
(or continuing the analogy of the language, each "program") may be very
different. We shouldn't refer to the AMBER trajectory as netCDF, but as
"AMBER netCDF". nMoldyn uses a "MMTK netCDF". These are not the same
thing...
According to the information page for nMoldyn
http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/nmoldyn-2/
converters exist for CHARMM and DL-POLY trajectories. You could use ptraj
to convert the AMBER netCDF to CHARMM trajectory and then use the nMoldyn
utility to convert that to MTTK format. Then to run nMoldyn, you would
need a corresponding PDB as well.
Reading the nMoldyn manual would have answered your questions...
--tec3
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Received on Thu May 06 2010 - 13:30:04 PDT
