Hello,
I use ptraj to convert to netcdf all the time, and it works just fine for
me. You need to trajout the trajectory as a netcdf file. For instance:
trajout mytrajectory.netcdf netcdf
You need a netcdf at the end to write to the proper format I believe.
It is also possible that box information is messing up nMOLDYN if it doesn't
know to expect that. To get rid of box information, simply put "nobox" at
the end of the trajout command.
Good luck!
Jason
On Thu, May 6, 2010 at 9:31 AM, Ganesh Kamath <gkamath9173.gmail.com> wrote:
> Hi amber folks,
>
> I know this question maybe slightly out but just wanted to see if
> anyone has tried this before.
>
> 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.
>
> Any help will be greatly appreciated.
>
> thanks,
> ganesh
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu May 06 2010 - 07:00:04 PDT
