All I can suggest now is that you try and find out what nMOLDYN expects when
it loads a trajectory file and compare it to what Amber produces.
Can you visualize the trajectory in VMD? Does it look OK?
All the best,
Jason
On Thu, May 6, 2010 at 9:59 AM, Ganesh Kamath <gkamath9173.gmail.com> wrote:
> Thank you Jason, I tried tried the nobox and yet the nMOLDYN displays
> "not a trajectory".
> This is a binary file, I dont know what else could be happening.
>
> regards,
> ganesh
>
> On Thu, May 6, 2010 at 9:37 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 07:30:05 PDT
